9-139915906-G-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139915906
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139915906
    reference: chr 9
allele count: 2
allele frequency: 1.820068070545839e-5
allele num: 109886
alternate allele: T
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.835C>A
  hgvsp: ENSP00000344155.6:p.Arg279Ser
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.835C>A
  hgvsp: ENSP00000265662.5:p.Arg279Ser
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.938C>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.832C>A
  hgvsp: ENSP00000360666.3:p.Arg278Ser
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.922C>A
  hgvsp: ENSP00000420527.1:p.Arg308Ser
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.922C>A
  hgvsp: ENSP00000418662.1:p.Arg308Ser
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1729C>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.879C>A
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1328
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 129
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 34
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5185
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20679
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 524
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 23353
  bin: 2.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 59
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 798
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4483
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3672
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 522
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 380
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 40907
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 795
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 96
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 213
  bin: 4.25e1
  variant carriers: 0
hgvs: p.Arg279Ser
num of homozygotes: 0
population: Other
population: European (Finnish)
population: European (Non-Finnish)
population: South Asian
population: East Asian
population: African
population: Latino
reference allele: G
site quality: VQSLOD
site quality: ReadPosRankSum
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: MQ
site quality: DP
site quality: QD
site quality: MQRankSum
site quality: FS
site quality: ClippingRankSum

9-139915910-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139915910
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139915910
    reference: chr 9
allele count: 1
allele frequency: 9.25754489909276e-6
allele num: 108020
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.918C>T
  hgvsp: ENST00000459850.1:c.918C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.831C>T
  hgvsp: ENST00000265662.5:c.831C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.934C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.828C>T
  hgvsp: ENST00000371605.3:c.828C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.918C>T
  hgvsp: ENST00000487109.1:c.918C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.831C>T
  hgvsp: ENST00000341511.6:c.831C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1725C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.875C>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 125
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4982
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14
  bin: 5.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 506
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1779
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 22265
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5378
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 34
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 824
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 19740
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4543
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 56
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1075
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 453
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 38860
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4989
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 487
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 112
  bin: 1.25e1
  variant carriers: 0
hgvs: p.Ala277Ala
num of homozygotes: 0
population: European (Non-Finnish)
population: East Asian
population: South Asian
population: Other
population: European (Finnish)
population: African
population: Latino
reference allele: G
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: MQ
site quality: InbreedingCoeff
site quality: FS
site quality: BaseQRankSum
site quality: VQSLOD
site quality: DP
site quality: ClippingRankSum
site quality: QD

9-139915914-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139915914
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139915914
    reference: chr 9
allele count: 3
allele frequency: 2.835324361106911e-5
allele num: 105808
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.914G>A
  hgvsp: ENSP00000418662.1:p.Arg305His
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.871G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.914G>A
  hgvsp: ENSP00000420527.1:p.Arg305His
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.930G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.824G>A
  hgvsp: ENSP00000360666.3:p.Arg275His
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.827G>A
  hgvsp: ENSP00000344155.6:p.Arg276His
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1721G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.827G>A
  hgvsp: ENSP00000265662.5:p.Arg276His
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5443
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 34
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 21137
  bin: 2.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 469
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2205
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 890
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 120
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4647
  bin: 3.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 18874
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6347
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 57
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 272
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 290
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1012
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 891
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 717
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 403
  bin: 4.25e1
  variant carriers: 0
hgvs: p.Arg276His
num of homozygotes: 0
population: European (Finnish)
population: African
population: East Asian
population: Other
population: European (Non-Finnish)
population: South Asian
population: Latino
reference allele: C
site quality: BaseQRankSum
site quality: MQ
site quality: QD
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: FS
site quality: VQSLOD
site quality: DP
site quality: ClippingRankSum

9-139915915-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139915915
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139915915
    reference: chr 9
allele count: 1
allele frequency: 9.448580823160362e-6
allele num: 105836
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.929C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.913C>T
  hgvsp: ENSP00000420527.1:p.Arg305Cys
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.826C>T
  hgvsp: ENSP00000265662.5:p.Arg276Cys
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.913C>T
  hgvsp: ENSP00000418662.1:p.Arg305Cys
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.870C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.826C>T
  hgvsp: ENSP00000344155.6:p.Arg276Cys
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1720C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.823C>T
  hgvsp: ENSP00000360666.3:p.Arg275Cys
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 5454
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 890
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2182
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6371
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 58
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4587
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 21162
  bin: 2.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 454
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18904
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 34
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 127
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 9.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 898
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 64
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 140
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 219
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1123
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 36295
  bin: 6.25e1
  variant carriers: 0
hgvs: p.Arg276Cys
num of homozygotes: 0
population: African
population: East Asian
population: Latino
population: Other
population: European (Non-Finnish)
population: South Asian
population: European (Finnish)
reference allele: G
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: MQ
site quality: DP
site quality: ReadPosRankSum
site quality: FS
site quality: VQSLOD
site quality: QD

9-139915916-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139915916
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139915916
    reference: chr 9
allele count: 5
allele frequency: 4.74842827024255e-5
allele num: 105298
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.822G>A
  hgvsp: ENST00000371605.3:c.822G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.869G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.912G>A
  hgvsp: ENST00000459850.1:c.912G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.912G>A
  hgvsp: ENST00000487109.1:c.912G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.825G>A
  hgvsp: ENST00000265662.5:c.825G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.825G>A
  hgvsp: ENST00000341511.6:c.825G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1719G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.928G>A
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 898
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5657
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4506
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2257
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6577
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20901
  bin: 2.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18763
  bin: 2.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 56
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 451
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 34
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 119
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 997
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1389
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 828
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 410
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 97
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 148
  bin: 1.25e1
  variant carriers: 0
hgvs: p.Ala275Ala
num of homozygotes: 0
population: South Asian
population: East Asian
population: Other
population: European (Non-Finnish)
population: Latino
population: African
population: European (Finnish)
reference allele: C
site quality: InbreedingCoeff
site quality: FS
site quality: VQSLOD
site quality: MQRankSum
site quality: DP
site quality: ReadPosRankSum
site quality: MQ
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: QD

9-139915922-A-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139915922
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139915922
    reference: chr 9
allele count: 2
allele frequency: 1.949317738791423e-5
allele num: 102600
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.906T>A
  hgvsp: ENST00000459850.1:c.906T>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.816T>A
  hgvsp: ENST00000371605.3:c.816T>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.922T>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.906T>A
  hgvsp: ENST00000487109.1:c.906T>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.819T>A
  hgvsp: ENST00000341511.6:c.819T>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.863T>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1713T>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.819T>A
  hgvsp: ENST00000265662.5:c.819T>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 19317
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 55
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 109
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18392
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6727
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7893
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 969
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 373
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 34
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3744
  bin: 3.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2591
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 9.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 418
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3870
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 218
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 962
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 630
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 34280
  bin: 6.25e1
  variant carriers: 0
hgvs: p.Ala273Ala
num of homozygotes: 0
population: East Asian
population: African
population: European (Non-Finnish)
population: European (Finnish)
population: Other
population: Latino
population: South Asian
reference allele: A
site quality: MQ
site quality: ClippingRankSum
site quality: MQRankSum
site quality: FS
site quality: VQSLOD
site quality: QD
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: DP
site quality: ReadPosRankSum

9-139915926-T-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139915926
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139915926
    reference: chr 9
allele count: 1
allele frequency: 9.939765023954834e-6
allele num: 100606
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.918A>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.902A>T
  hgvsp: ENSP00000420527.1:p.Gln301Leu
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.812A>T
  hgvsp: ENSP00000360666.3:p.Gln271Leu
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.859A>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.815A>T
  hgvsp: ENSP00000265662.5:p.Gln272Leu
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1709A>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.815A>T
  hgvsp: ENSP00000344155.6:p.Gln272Leu
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.902A>T
  hgvsp: ENSP00000418662.1:p.Gln301Leu
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 358
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17934
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2780
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 108
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3467
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7475
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1023
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8817
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 34
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 54
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18145
  bin: 2.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 640
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 145
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1477
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 62
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1143
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 32785
  bin: 6.25e1
  variant carriers: 0
hgvs: p.Gln272Leu
num of homozygotes: 0
population: Latino
population: Other
population: African
population: European (Finnish)
population: East Asian
population: European (Non-Finnish)
population: South Asian
reference allele: T
site quality: ReadPosRankSum
site quality: DP
site quality: QD
site quality: VQSLOD
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: MQ
site quality: MQRankSum
site quality: FS

http://identifiers.org/exac.variant/9-139915940-A-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139915940
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139915940
    reference: chr 9
allele count: 2034
allele frequency: 2.248109996021044e-2
allele num: 90476
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.888T>G
  hgvsp: ENST00000487109.1:c.888T>G(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.888T>G
  hgvsp: ENST00000459850.1:c.888T>G(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.798T>G
  hgvsp: ENST00000371605.3:c.798T>G(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.904T>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.801T>G
  hgvsp: ENST00000265662.5:c.801T>G(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.845T>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1695T>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.801T>G
  hgvsp: ENST00000341511.6:c.801T>G(p.%3D)
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 242
  bin: 9.75e1
  variant carriers: 240
genotype depth: GenotypeDepth
  all individuals: 34
  bin: 5.25e1
  variant carriers: 12
genotype depth: GenotypeDepth
  all individuals: 3505
  bin: 1.75e1
  variant carriers: 445
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 6.25e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 9
  bin: 9.25e1
  variant carriers: 8
genotype depth: GenotypeDepth
  all individuals: 13433
  bin: 2.75e1
  variant carriers: 273
genotype depth: GenotypeDepth
  all individuals: 11203
  bin: 1.25e1
  variant carriers: 227
genotype depth: GenotypeDepth
  all individuals: 62
  bin: 4.75e1
  variant carriers: 27
genotype depth: GenotypeDepth
  all individuals: 303
  bin: 3.75e1
  variant carriers: 87
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 7.75e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 9
  bin: 7.25e1
  variant carriers: 5
genotype depth: GenotypeDepth
  all individuals: 13852
  bin: 2.25e1
  variant carriers: 419
genotype depth: GenotypeDepth
  all individuals: 15
  bin: 5.75e1
  variant carriers: 5
genotype depth: GenotypeDepth
  all individuals: 1351
  bin: 2.5e0
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 13405
  bin: 7.5e0
  variant carriers: 59
genotype depth: GenotypeDepth
  all individuals: 117
  bin: 4.25e1
  variant carriers: 50
genotype depth: GenotypeDepth
  all individuals: 12
  bin: 6.75e1
  variant carriers: 5
genotype depth: GenotypeDepth
  all individuals: 2581
  bin: 3.25e1
  variant carriers: 195
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 8.75e1
  variant carriers: 6
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 149
  bin: 8.25e1
  variant carriers: 13
genotype quality: GenotypeQuality
  all individuals: 20651
  bin: 2.25e1
  variant carriers: 4
genotype quality: GenotypeQuality
  all individuals: 1272
  bin: 3.75e1
  variant carriers: 3
genotype quality: GenotypeQuality
  all individuals: 59
  bin: 9.25e1
  variant carriers: 17
genotype quality: GenotypeQuality
  all individuals: 1369
  bin: 7.5e0
  variant carriers: 3
genotype quality: GenotypeQuality
  all individuals: 132
  bin: 2.5e0
  variant carriers: 1
hgvs: p.Ala267Ala
num of homozygotes: 28
population: East Asian
population: African
population: European (Non-Finnish)
population: Other
population: European (Finnish)
population: South Asian
population: Latino
reference allele: A
site quality: ReadPosRankSum
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: FS
site quality: DP
site quality: ClippingRankSum
site quality: MQRankSum
site quality: QD
site quality: MQ

9-139915940-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139915940
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139915940
    reference: chr 9
allele count: 1
allele frequency: 1.105265484769442e-5
allele num: 90476
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.798T>C
  hgvsp: ENST00000371605.3:c.798T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.845T>C
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.801T>C
  hgvsp: ENST00000341511.6:c.801T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.888T>C
  hgvsp: ENST00000487109.1:c.888T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1695T>C
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.801T>C
  hgvsp: ENST00000265662.5:c.801T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.888T>C
  hgvsp: ENST00000459850.1:c.888T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.904T>C
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 12
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 303
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 62
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2581
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 117
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13405
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3505
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13852
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1351
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11203
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 242
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 34
  bin: 5.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13433
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 511
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2184
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2481
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 444
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 132
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2058
  bin: 9.75e1
  variant carriers: 1
hgvs: p.Ala267Ala
num of homozygotes: 0
population: European (Finnish)
population: Latino
population: East Asian
population: Other
population: South Asian
population: African
population: European (Non-Finnish)
reference allele: A
site quality: DP
site quality: ClippingRankSum
site quality: MQRankSum
site quality: QD
site quality: BaseQRankSum
site quality: FS
site quality: MQ
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: ReadPosRankSum

9-139915946-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139915946
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139915946
    reference: chr 9
allele count: 1
allele frequency: 1.17827265229174e-5
allele num: 84870
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.882G>A
  hgvsp: ENST00000487109.1:c.882G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.795G>A
  hgvsp: ENST00000341511.6:c.795G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.792G>A
  hgvsp: ENST00000371605.3:c.792G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1689G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.882G>A
  hgvsp: ENST00000459850.1:c.882G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.839G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.898G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.795G>A
  hgvsp: ENST00000265662.5:c.795G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12945
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 214
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3308
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 39
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11456
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15853
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1587
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2088
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 69
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 22
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12490
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 285
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 350
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 24458
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 374
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 136
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2394
  bin: 3.25e1
  variant carriers: 0
hgvs: p.Arg265Arg
num of homozygotes: 0
population: African
population: South Asian
population: European (Non-Finnish)
population: European (Finnish)
population: East Asian
population: Latino
population: Other
reference allele: C
site quality: QD
site quality: VQSLOD
site quality: ClippingRankSum
site quality: FS
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: DP
site quality: BaseQRankSum
site quality: MQ

9-139915947-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139915947
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139915947
    reference: chr 9
allele count: 1
allele frequency: 1.199644905108088e-5
allele num: 83358
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.897G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.794G>A
  hgvsp: ENSP00000344155.6:p.Arg265Gln
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.791G>A
  hgvsp: ENSP00000360666.3:p.Arg264Gln
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.881G>A
  hgvsp: ENSP00000420527.1:p.Arg294Gln
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.881G>A
  hgvsp: ENSP00000418662.1:p.Arg294Gln
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.794G>A
  hgvsp: ENSP00000265662.5:p.Arg265Gln
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1688G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.838G>A
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 13315
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 22
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16352
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 38
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12123
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1993
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10921
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 210
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1650
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3372
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 8.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 68
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 324
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 165
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 20281
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 236
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 508
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 347
  bin: 7.75e1
  variant carriers: 0
hgvs: p.Arg265Gln
num of homozygotes: 0
population: European (Finnish)
population: African
population: Other
population: South Asian
population: East Asian
population: Latino
population: European (Non-Finnish)
reference allele: C
site quality: MQRankSum
site quality: MQ
site quality: ReadPosRankSum
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: FS
site quality: DP
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: QD

9-139915948-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139915948
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139915948
    reference: chr 9
allele count: 1
allele frequency: 1.216130758379141e-5
allele num: 82228
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.837C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1687C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.880C>T
  hgvsp: ENSP00000420527.1:p.Arg294Trp
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.793C>T
  hgvsp: ENSP00000265662.5:p.Arg265Trp
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.880C>T
  hgvsp: ENSP00000418662.1:p.Arg294Trp
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.896C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.790C>T
  hgvsp: ENSP00000360666.3:p.Arg264Trp
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.793C>T
  hgvsp: ENSP00000344155.6:p.Arg265Trp
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 16797
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3333
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1715
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13590
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11932
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 38
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 205
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 67
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 22
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10498
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1863
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1847
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 323
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 109
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 25727
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 19728
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 625
  bin: 4.75e1
  variant carriers: 0
hgvs: p.Arg265Trp
num of homozygotes: 0
population: European (Finnish)
population: European (Non-Finnish)
population: East Asian
population: Latino
population: Other
population: African
population: South Asian
reference allele: G
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: VQSLOD
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: FS
site quality: DP
site quality: MQ
site quality: QD
site quality: ReadPosRankSum

9-139915953-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139915953
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139915953
    reference: chr 9
allele count: 150
allele frequency: 1.937684079987599e-3
allele num: 77412
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.788G>A
  hgvsp: ENSP00000265662.5:p.Gly263Asp
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1682G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.891G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.785G>A
  hgvsp: ENSP00000360666.3:p.Gly262Asp
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.875G>A
  hgvsp: ENSP00000418662.1:p.Gly292Asp
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.832G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.788G>A
  hgvsp: ENSP00000344155.6:p.Gly263Asp
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.875G>A
  hgvsp: ENSP00000420527.1:p.Gly292Asp
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 10623
  bin: 2.25e1
  variant carriers: 17
genotype depth: GenotypeDepth
  all individuals: 171
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 8286
  bin: 2.75e1
  variant carriers: 7
genotype depth: GenotypeDepth
  all individuals: 38
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18892
  bin: 7.5e0
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 2088
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14854
  bin: 1.25e1
  variant carriers: 27
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1402
  bin: 3.25e1
  variant carriers: 5
genotype depth: GenotypeDepth
  all individuals: 23
  bin: 5.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 8.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 60
  bin: 4.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3535
  bin: 1.75e1
  variant carriers: 30
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 9.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 68
  bin: 9.75e1
  variant carriers: 58
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 28270
  bin: 2.25e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 2170
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 899
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 33
  bin: 9.25e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 2571
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 31
  bin: 8.75e1
  variant carriers: 0
hgvs: p.Gly263Asp
num of homozygotes: 1
population: European (Finnish)
population: Latino
population: South Asian
population: European (Non-Finnish)
population: East Asian
population: African
population: Other
reference allele: C
site quality: DP
site quality: VQSLOD
site quality: ClippingRankSum
site quality: QD
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: FS
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: MQ

9-139915956-T-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139915956
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139915956
    reference: chr 9
allele count: 2
allele frequency: 2.647393640960474e-5
allele num: 75546
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.829A>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.872A>G
  hgvsp: ENSP00000420527.1:p.Gln291Arg
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.782A>G
  hgvsp: ENSP00000360666.3:p.Gln261Arg
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.872A>G
  hgvsp: ENSP00000418662.1:p.Gln291Arg
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.785A>G
  hgvsp: ENSP00000344155.6:p.Gln262Arg
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1679A>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.785A>G
  hgvsp: ENSP00000265662.5:p.Gln262Arg
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.888A>G
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 3322
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10539
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14965
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7744
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 37
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2220
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 19658
  bin: 7.5e0
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 166
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 22
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1286
  bin: 3.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 58
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 873
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 607
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 472
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 273
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2334
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 695
  bin: 5.25e1
  variant carriers: 0
hgvs: p.Gln262Arg
num of homozygotes: 0
population: East Asian
population: African
population: European (Non-Finnish)
population: Latino
population: Other
population: South Asian
population: European (Finnish)
reference allele: T
site quality: ClippingRankSum
site quality: MQ
site quality: BaseQRankSum
site quality: MQRankSum
site quality: FS
site quality: QD
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: DP
site quality: ReadPosRankSum

http://identifiers.org/exac.variant/9-139915958-C-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139915958
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139915958
    reference: chr 9
allele count: 1
allele frequency: 1.349272741992066e-5
allele num: 74114
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.827G>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.780G>T
  hgvsp: ENST00000371605.3:c.780G>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1677G>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.870G>T
  hgvsp: ENST00000459850.1:c.870G>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.783G>T
  hgvsp: ENST00000265662.5:c.783G>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.870G>T
  hgvsp: ENST00000487109.1:c.870G>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.783G>T
  hgvsp: ENST00000341511.6:c.783G>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.886G>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: VQSRTrancheSNP99.60to99.80
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3192
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20255
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 58
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1177
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 37
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7287
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2339
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15129
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 10356
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 22
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 152
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 555
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 462
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 320
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1394
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2442
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1532
  bin: 6.75e1
  variant carriers: 0
hgvs: p.Leu261Leu
num of homozygotes: 0
population: East Asian
population: European (Finnish)
population: European (Non-Finnish)
population: African
population: South Asian
population: Latino
population: Other
reference allele: C
site quality: BaseQRankSum
site quality: QD
site quality: MQRankSum
site quality: MQ
site quality: InbreedingCoeff
site quality: FS
site quality: ClippingRankSum
site quality: DP
site quality: ReadPosRankSum
site quality: VQSLOD

http://identifiers.org/exac.variant/9-139915963-C-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139915963
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139915963
    reference: chr 9
allele count: 1
allele frequency: 1.430205949656751e-5
allele num: 69920
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.778G>T
  hgvsp: ENSP00000265662.5:p.Ala260Ser
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.822G>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1672G>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.865G>T
  hgvsp: ENSP00000418662.1:p.Ala289Ser
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.881G>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.865G>T
  hgvsp: ENSP00000420527.1:p.Ala289Ser
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.775G>T
  hgvsp: ENSP00000360666.3:p.Ala259Ser
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.778G>T
  hgvsp: ENSP00000344155.6:p.Ala260Ser
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3077
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1005
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 21771
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 142
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 37
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 57
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2805
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9485
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5984
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15562
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 22
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 214
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2537
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 680
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 80
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1172
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13327
  bin: 6.25e1
  variant carriers: 0
hgvs: p.Ala260Ser
num of homozygotes: 0
population: African
population: European (Non-Finnish)
population: Other
population: East Asian
population: Latino
population: European (Finnish)
population: South Asian
reference allele: C
site quality: MQRankSum
site quality: ClippingRankSum
site quality: MQ
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: QD
site quality: FS
site quality: VQSLOD
site quality: ReadPosRankSum
site quality: DP

9-139915973-ACT-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139915973
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139915971
    reference: chr 9
allele count: 1
allele frequency: 1.578233010321644e-5
allele num: 63362
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.869_870delAG
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: frameshift_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.766_767delAG
  hgvsp: ENSP00000265662.5:p.Gln257GlufsTer29
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: frameshift_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.853_854delAG
  hgvsp: ENSP00000420527.1:p.Gln286GlufsTer29
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: frameshift_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.763_764delAG
  hgvsp: ENSP00000360666.3:p.Gln256GlufsTer29
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1660_*1661delAG
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.810_811delAG
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: frameshift_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.853_854delAG
  hgvsp: ENSP00000418662.1:p.Gln286GlufsTer29
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: frameshift_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.766_767delAG
  hgvsp: ENSP00000344155.6:p.Gln257GlufsTer29
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: frameshift
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4682
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 853
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4122
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2621
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 22
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 57
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15925
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 23586
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 137
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7832
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 37
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 350
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 32814
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4304
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 539
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 194
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2498
  bin: 2.75e1
  variant carriers: 0
hgvs: p.Gln257GlufsTer29
num of homozygotes: 0
population: Other
population: Latino
population: European (Finnish)
population: African
population: South Asian
population: East Asian
population: European (Non-Finnish)
reference allele: ACT
site quality: DP
site quality: FS
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: MQ
site quality: MQRankSum
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: ClippingRankSum
site quality: QD

http://identifiers.org/exac.variant/9-139915985-A-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139915985
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139915985
    reference: chr 9
allele count: 1
allele frequency: 1.778979577314453e-5
allele num: 56212
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.800T>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.843T>G
  hgvsp: ENST00000459850.1:c.843T>G(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.753T>G
  hgvsp: ENST00000371605.3:c.753T>G(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.756T>G
  hgvsp: ENST00000265662.5:c.756T>G(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.859T>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1650T>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.843T>G
  hgvsp: ENST00000487109.1:c.843T>G(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.756T>G
  hgvsp: ENST00000341511.6:c.756T>G(p.%3D)
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 5932
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 22
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15775
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1827
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 37
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 25146
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6273
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3802
  bin: 2.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 754
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 56
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 134
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 150
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 735
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 23
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 137
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1874
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 66
  bin: 8.25e1
  variant carriers: 0
hgvs: p.Thr252Thr
num of homozygotes: 0
population: East Asian
population: African
population: European (Non-Finnish)
population: Other
population: European (Finnish)
population: Latino
population: South Asian
reference allele: A
site quality: FS
site quality: MQ
site quality: MQRankSum
site quality: BaseQRankSum
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: QD
site quality: DP
site quality: ReadPosRankSum

9-139915995-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139915995
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139915995
    reference: chr 9
allele count: 2
allele frequency: 4.213009774182676e-5
allele num: 47472
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.833G>A
  hgvsp: ENSP00000418662.1:p.Arg278Gln
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.743G>A
  hgvsp: ENSP00000360666.3:p.Arg248Gln
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.746G>A
  hgvsp: ENSP00000344155.6:p.Arg249Gln
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.746G>A
  hgvsp: ENSP00000265662.5:p.Arg249Gln
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1640G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.849G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.833G>A
  hgvsp: ENSP00000420527.1:p.Arg278Gln
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.790G>A
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2972
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4708
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1636
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 37
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 25779
  bin: 7.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 22
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 131
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 681
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9459
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14088
  bin: 1.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 55
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 177
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 62
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 642
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 28
  bin: 9.25e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 2037
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2341
  bin: 1.75e1
  variant carriers: 0
hgvs: p.Arg249Gln
num of homozygotes: 0
population: European (Finnish)
population: South Asian
population: European (Non-Finnish)
population: East Asian
population: African
population: Latino
population: Other
reference allele: C
site quality: MQRankSum
site quality: DP
site quality: BaseQRankSum
site quality: QD
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: MQ
site quality: FS

9-139915996-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139915996
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139915996
    reference: chr 9
allele count: 2
allele frequency: 4.23674956573317e-5
allele num: 47206
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.832C>T
  hgvsp: ENSP00000420527.1:p.Arg278Trp
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.745C>T
  hgvsp: ENSP00000344155.6:p.Arg249Trp
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.745C>T
  hgvsp: ENSP00000265662.5:p.Arg249Trp
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.742C>T
  hgvsp: ENSP00000360666.3:p.Arg248Trp
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.832C>T
  hgvsp: ENSP00000418662.1:p.Arg278Trp
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.789C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.848C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1639C>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 37
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 22
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 129
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 55
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 25961
  bin: 7.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 9514
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13992
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1506
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2965
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4711
  bin: 2.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 679
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 33002
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1235
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9966
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 594
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 28
  bin: 9.25e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 1954
  bin: 1.75e1
  variant carriers: 0
hgvs: p.Arg249Trp
num of homozygotes: 0
population: African
population: Other
population: East Asian
population: Latino
population: South Asian
population: European (Finnish)
population: European (Non-Finnish)
reference allele: G
site quality: MQ
site quality: BaseQRankSum
site quality: VQSLOD
site quality: DP
site quality: QD
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: FS
site quality: ReadPosRankSum

9-139915997-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139915997
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139915997
    reference: chr 9
allele count: 1
allele frequency: 2.152018593440647e-5
allele num: 46468
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.744C>T
  hgvsp: ENST00000265662.5:c.744C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.741C>T
  hgvsp: ENST00000371605.3:c.741C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.744C>T
  hgvsp: ENST00000341511.6:c.744C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1638C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.788C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.831C>T
  hgvsp: ENST00000459850.1:c.831C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.831C>T
  hgvsp: ENST00000487109.1:c.831C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.847C>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 26085
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1416
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9766
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2927
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13822
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 129
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 37
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 676
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4611
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 22
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 55
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 9.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1262
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 557
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1442
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10246
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 22
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1965
  bin: 2.75e1
  variant carriers: 0
hgvs: p.Gly248Gly
num of homozygotes: 0
population: South Asian
population: European (Finnish)
population: Latino
population: East Asian
population: Other
population: African
population: European (Non-Finnish)
reference allele: G
site quality: ReadPosRankSum
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: FS
site quality: InbreedingCoeff
site quality: QD
site quality: MQRankSum
site quality: VQSLOD
site quality: MQ
site quality: DP

9-139916005-C-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916005
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916005
    reference: chr 9
allele count: 1
allele frequency: 2.531389226407453e-5
allele num: 39504
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.733G>C
  hgvsp: ENSP00000360666.3:p.Glu245Gln
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1630G>C
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.823G>C
  hgvsp: ENSP00000420527.1:p.Glu275Gln
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.736G>C
  hgvsp: ENSP00000265662.5:p.Glu246Gln
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.839G>C
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.780G>C
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.736G>C
  hgvsp: ENSP00000344155.6:p.Glu246Gln
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.823G>C
  hgvsp: ENSP00000418662.1:p.Glu275Gln
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 34
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 602
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4002
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 115
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 21
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11851
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 25328
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13565
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2576
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1077
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 54
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 9.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 159
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 761
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1558
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 63
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 91
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6036
  bin: 6.25e1
  variant carriers: 0
hgvs: p.Glu246Gln
num of homozygotes: 0
population: South Asian
population: European (Non-Finnish)
population: Latino
population: African
population: European (Finnish)
population: Other
population: East Asian
reference allele: C
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: FS
site quality: QD
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: DP
site quality: MQ
site quality: ClippingRankSum

http://identifiers.org/exac.variant/9-139916006-C-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916006
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916006
    reference: chr 9
allele count: 1
allele frequency: 2.529596276434281e-5
allele num: 39532
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.779G>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.838G>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.732G>T
  hgvsp: ENST00000371605.3:c.732G>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1629G>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.735G>T
  hgvsp: ENST00000265662.5:c.735G>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.822G>T
  hgvsp: ENST00000487109.1:c.822G>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.822G>T
  hgvsp: ENST00000459850.1:c.822G>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.735G>T
  hgvsp: ENST00000341511.6:c.735G>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 25362
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13604
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 603
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 34
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 117
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4012
  bin: 2.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2566
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11816
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1040
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 54
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 21
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6107
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1531
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 29742
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 14211
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 62
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 657
  bin: 6.75e1
  variant carriers: 0
hgvs: p.Gly245Gly
num of homozygotes: 0
population: South Asian
population: East Asian
population: European (Finnish)
population: European (Non-Finnish)
population: African
population: Other
population: Latino
reference allele: C
site quality: VQSLOD
site quality: FS
site quality: BaseQRankSum
site quality: QD
site quality: ClippingRankSum
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: MQ
site quality: DP
site quality: InbreedingCoeff

9-139916009-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916009
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916009
    reference: chr 9
allele count: 10
allele frequency: 2.800336040324839e-4
allele num: 35710
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.819G>A
  hgvsp: ENST00000459850.1:c.819G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.835G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.732G>A
  hgvsp: ENST00000265662.5:c.732G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.729G>A
  hgvsp: ENST00000371605.3:c.729G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.776G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1626G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.819G>A
  hgvsp: ENST00000487109.1:c.819G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.732G>A
  hgvsp: ENST00000341511.6:c.732G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 20
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15598
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2504
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 897
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 592
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 24794
  bin: 7.5e0
  variant carriers: 8
genotype depth: GenotypeDepth
  all individuals: 108
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 6.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 10601
  bin: 1.25e1
  variant carriers: 6
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3834
  bin: 2.25e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 645
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 352
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 73
  bin: 4.25e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 64
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 977
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 27148
  bin: 2.25e1
  variant carriers: 0
hgvs: p.Ser244Ser
num of homozygotes: 0
population: European (Finnish)
population: East Asian
population: African
population: South Asian
population: European (Non-Finnish)
population: Latino
population: Other
reference allele: C
site quality: InbreedingCoeff
site quality: QD
site quality: FS
site quality: MQRankSum
site quality: BaseQRankSum
site quality: DP
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: MQ
site quality: ClippingRankSum

9-139916010-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916010
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916010
    reference: chr 9
allele count: 1
allele frequency: 2.803790725060282e-5
allele num: 35666
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1625C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.728C>T
  hgvsp: ENSP00000360666.3:p.Ser243Leu
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.834C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.731C>T
  hgvsp: ENSP00000265662.5:p.Ser244Leu
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.818C>T
  hgvsp: ENSP00000420527.1:p.Ser273Leu
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.731C>T
  hgvsp: ENSP00000344155.6:p.Ser244Leu
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.775C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.818C>T
  hgvsp: ENSP00000418662.1:p.Ser273Leu
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 109
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 812
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 24923
  bin: 7.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2502
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3833
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 592
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15709
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10454
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 9.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 645
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1562
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 60
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 26
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 26
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 851
  bin: 2.5e0
  variant carriers: 0
hgvs: p.Ser244Leu
num of homozygotes: 0
population: European (Finnish)
population: African
population: South Asian
population: European (Non-Finnish)
population: Latino
population: East Asian
population: Other
reference allele: G
site quality: InbreedingCoeff
site quality: MQ
site quality: BaseQRankSum
site quality: VQSLOD
site quality: MQRankSum
site quality: DP
site quality: FS
site quality: ReadPosRankSum
site quality: QD
site quality: ClippingRankSum

9-139916016-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916016
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916016
    reference: chr 9
allele count: 50
allele frequency: 1.580877703300873e-3
allele num: 31628
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.722C>T
  hgvsp: ENSP00000360666.3:p.Pro241Leu
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.828C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.769C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.812C>T
  hgvsp: ENSP00000420527.1:p.Pro271Leu
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.812C>T
  hgvsp: ENSP00000418662.1:p.Pro271Leu
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1619C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.725C>T
  hgvsp: ENSP00000344155.6:p.Pro242Leu
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.725C>T
  hgvsp: ENSP00000265662.5:p.Pro242Leu
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 7.25e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 8756
  bin: 1.25e1
  variant carriers: 25
genotype depth: GenotypeDepth
  all individuals: 18262
  bin: 2.5e0
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 104
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 610
  bin: 1.75e1
  variant carriers: 4
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 577
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 4.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 3698
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 24231
  bin: 7.5e0
  variant carriers: 15
genotype depth: GenotypeDepth
  all individuals: 2422
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 5.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 9.75e1
  variant carriers: 8
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2521
  bin: 1.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 1573
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 28
  bin: 9.25e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 18744
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 155
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 43
  bin: 4.75e1
  variant carriers: 0
hgvs: p.Pro242Leu
num of homozygotes: 0
population: European (Finnish)
population: East Asian
population: European (Non-Finnish)
population: Latino
population: South Asian
population: Other
population: African
reference allele: G
site quality: MQ
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: FS
site quality: QD
site quality: MQRankSum
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: DP
site quality: VQSLOD

9-139916018-C-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916018
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916018
    reference: chr 9
allele count: 2
allele frequency: 6.605892456070815e-5
allele num: 30276
alternate allele: G
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.723G>C
  hgvsp: ENST00000341511.6:c.723G>C(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.810G>C
  hgvsp: ENST00000459850.1:c.810G>C(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.826G>C
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.720G>C
  hgvsp: ENST00000371605.3:c.720G>C(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.723G>C
  hgvsp: ENST00000265662.5:c.723G>C(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.810G>C
  hgvsp: ENST00000487109.1:c.810G>C(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.767G>C
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1617G>C
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 20
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 8158
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2412
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 49
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 518
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 23908
  bin: 7.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3656
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 107
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 19246
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 570
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 149
  bin: 9.75e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 54
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 19704
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 117
  bin: 7.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 996
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1026
  bin: 2.75e1
  variant carriers: 0
hgvs: p.Thr241Thr
num of homozygotes: 0
population: European (Finnish)
population: Other
population: South Asian
population: African
population: European (Non-Finnish)
population: East Asian
population: Latino
reference allele: C
site quality: MQ
site quality: FS
site quality: QD
site quality: DP
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: MQRankSum
site quality: InbreedingCoeff

9-139916018-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916018
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916018
    reference: chr 9
allele count: 10
allele frequency: 3.302946228035407e-4
allele num: 30276
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.810G>A
  hgvsp: ENST00000459850.1:c.810G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.767G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.826G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.720G>A
  hgvsp: ENST00000371605.3:c.720G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.723G>A
  hgvsp: ENST00000341511.6:c.723G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1617G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.810G>A
  hgvsp: ENST00000487109.1:c.810G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.723G>A
  hgvsp: ENST00000265662.5:c.723G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 20
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 19246
  bin: 2.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3656
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2412
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8158
  bin: 1.25e1
  variant carriers: 7
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 6.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 23908
  bin: 7.5e0
  variant carriers: 10
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 518
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 49
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 107
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 570
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 19704
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 149
  bin: 9.75e1
  variant carriers: 10
genotype quality: GenotypeQuality
  all individuals: 1571
  bin: 1.25e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 702
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 220
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 54
  bin: 5.25e1
  variant carriers: 3
hgvs: p.Thr241Thr
num of homozygotes: 0
population: European (Non-Finnish)
population: South Asian
population: East Asian
population: Other
population: Latino
population: African
population: European (Finnish)
reference allele: C
site quality: QD
site quality: FS
site quality: ReadPosRankSum
site quality: InbreedingCoeff
site quality: DP
site quality: MQ
site quality: BaseQRankSum
site quality: MQRankSum
site quality: VQSLOD
site quality: ClippingRankSum

9-139916019-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916019
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916019
    reference: chr 9
allele count: 1
allele frequency: 3.447800303406427e-5
allele num: 29004
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.809C>T
  hgvsp: ENSP00000420527.1:p.Thr270Met
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.809C>T
  hgvsp: ENSP00000418662.1:p.Thr270Met
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.722C>T
  hgvsp: ENSP00000265662.5:p.Thr241Met
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1616C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.766C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.719C>T
  hgvsp: ENSP00000360666.3:p.Thr240Met
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.722C>T
  hgvsp: ENSP00000344155.6:p.Thr241Met
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.825C>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20152
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2399
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 107
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 23482
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33
  bin: 4.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 563
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3611
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 49
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 495
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7665
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 115
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2781
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 978
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 202
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 33
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1016
  bin: 2.5e0
  variant carriers: 0
hgvs: p.Thr241Met
num of homozygotes: 0
population: Latino
population: South Asian
population: European (Non-Finnish)
population: Other
population: African
population: European (Finnish)
population: East Asian
reference allele: G
site quality: VQSLOD
site quality: FS
site quality: BaseQRankSum
site quality: QD
site quality: InbreedingCoeff
site quality: MQ
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: ClippingRankSum
site quality: DP

9-139916036-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916036
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916036
    reference: chr 9
allele count: 19
allele frequency: 9.427408951076709e-4
allele num: 20154
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.792G>A
  hgvsp: ENST00000487109.1:c.792G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.705G>A
  hgvsp: ENST00000341511.6:c.705G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.749G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.705G>A
  hgvsp: ENST00000265662.5:c.705G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1599G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.702G>A
  hgvsp: ENST00000371605.3:c.702G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.792G>A
  hgvsp: ENST00000459850.1:c.792G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.808G>A
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 2292
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 19
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 28878
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17139
  bin: 7.5e0
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 7.25e1
  variant carriers: 4
genotype depth: GenotypeDepth
  all individuals: 3272
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 106
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33
  bin: 4.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 49
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 543
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 233
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 5.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 3943
  bin: 1.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 9.75e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 9
  bin: 6.75e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 36
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5164
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 528
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 155
  bin: 9.75e1
  variant carriers: 18
genotype quality: GenotypeQuality
  all individuals: 58
  bin: 8.25e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 307
  bin: 3.25e1
  variant carriers: 0
hgvs: p.Leu235Leu
num of homozygotes: 0
population: South Asian
population: Latino
population: European (Non-Finnish)
population: African
population: East Asian
population: Other
population: European (Finnish)
reference allele: C
site quality: MQ
site quality: ReadPosRankSum
site quality: BaseQRankSum
site quality: FS
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: DP
site quality: ClippingRankSum
site quality: QD
site quality: VQSLOD

9-139916038-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916038
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916038
    reference: chr 9
allele count: 2
allele frequency: 9.8833761612967e-5
allele num: 20236
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.790C>T
  hgvsp: ENST00000459850.1:c.790C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.700C>T
  hgvsp: ENST00000371605.3:c.700C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.747C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.703C>T
  hgvsp: ENST00000341511.6:c.703C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1597C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.703C>T
  hgvsp: ENST00000265662.5:c.703C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.790C>T
  hgvsp: ENST00000487109.1:c.790C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.806C>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: VQSRTrancheSNP99.60to99.80
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 105
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17139
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3277
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3790
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 545
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 200
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29110
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 49
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2303
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 19
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 14244
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 56
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 113
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 299
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 593
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21
  bin: 8.75e1
  variant carriers: 0
hgvs: p.Leu235Leu
num of homozygotes: 0
population: European (Finnish)
population: European (Non-Finnish)
population: African
population: Latino
population: South Asian
population: Other
population: East Asian
reference allele: G
site quality: FS
site quality: MQRankSum
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: MQ
site quality: InbreedingCoeff
site quality: DP
site quality: VQSLOD
site quality: QD
site quality: ClippingRankSum

9-139916039-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916039
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916039
    reference: chr 9
allele count: 0
allele frequency: 0.0e0
allele num: 20258
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.805C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.702C>T
  hgvsp: ENST00000265662.5:c.702C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.789C>T
  hgvsp: ENST00000459850.1:c.789C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.699C>T
  hgvsp: ENST00000371605.3:c.699C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.702C>T
  hgvsp: ENST00000341511.6:c.702C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1596C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.789C>T
  hgvsp: ENST00000487109.1:c.789C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.746C>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: AC_Adj0_Filter
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3757
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17144
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 49
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29159
  bin: 2.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 105
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 544
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 19
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3280
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2305
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 193
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 148
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1612
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 29106
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 56
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 24
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2272
  bin: 1.75e1
  variant carriers: 0
hgvs: p.Leu234Leu
num of homozygotes: 0
population: European (Non-Finnish)
population: African
population: European (Finnish)
population: East Asian
population: Latino
population: South Asian
population: Other
reference allele: G
site quality: ReadPosRankSum
site quality: FS
site quality: MQ
site quality: MQRankSum
site quality: DP
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: VQSLOD
site quality: QD

9-139916042-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916042
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916042
    reference: chr 9
allele count: 0
allele frequency: 0.0e0
allele num: 19768
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.743C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.699C>T
  hgvsp: ENST00000265662.5:c.699C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.699C>T
  hgvsp: ENST00000341511.6:c.699C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.802C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.786C>T
  hgvsp: ENST00000459850.1:c.786C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.696C>T
  hgvsp: ENST00000371605.3:c.696C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.786C>T
  hgvsp: ENST00000487109.1:c.786C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1593C>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: AC_Adj0_Filter
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2306
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16463
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3502
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29936
  bin: 2.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 541
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 105
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 49
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 176
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3252
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 19
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5213
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 56
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1652
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 84
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 493
  bin: 2.75e1
  variant carriers: 0
hgvs: p.Ala233Ala
num of homozygotes: 0
population: Latino
population: European (Finnish)
population: Other
population: South Asian
population: African
population: East Asian
population: European (Non-Finnish)
reference allele: G
site quality: FS
site quality: QD
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: DP
site quality: MQ

9-139916045-A-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916045
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916045
    reference: chr 9
allele count: 1
allele frequency: 5.609154139555755e-5
allele num: 17828
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.693T>A
  hgvsp: ENST00000371605.3:c.693T>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.696T>A
  hgvsp: ENST00000265662.5:c.696T>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.740T>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.696T>A
  hgvsp: ENST00000341511.6:c.696T>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.783T>A
  hgvsp: ENST00000459850.1:c.783T>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1590T>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.799T>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.783T>A
  hgvsp: ENST00000487109.1:c.783T>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: VQSRTrancheSNP99.60to99.80
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3196
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 545
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2811
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 102
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 49
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 31433
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 167
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14930
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2273
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 19
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2541
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5114
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 79
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 20
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 30548
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11391
  bin: 2.25e1
  variant carriers: 0
hgvs: p.Pro232Pro
num of homozygotes: 0
population: East Asian
population: South Asian
population: European (Non-Finnish)
population: African
population: Other
population: Latino
population: European (Finnish)
reference allele: A
site quality: ClippingRankSum
site quality: VQSLOD
site quality: MQ
site quality: MQRankSum
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: DP
site quality: InbreedingCoeff
site quality: FS
site quality: QD

9-139916047-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916047
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916047
    reference: chr 9
allele count: 1
allele frequency: 5.509034817100044e-5
allele num: 18152
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.781C>T
  hgvsp: ENSP00000418662.1:p.Pro261Ser
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1588C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.694C>T
  hgvsp: ENSP00000344155.6:p.Pro232Ser
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.797C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.781C>T
  hgvsp: ENSP00000420527.1:p.Pro261Ser
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.694C>T
  hgvsp: ENSP00000265662.5:p.Pro232Ser
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.691C>T
  hgvsp: ENSP00000360666.3:p.Pro231Ser
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.738C>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2802
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3194
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 102
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2280
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 19
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 31771
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 50
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 541
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14827
  bin: 7.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 159
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 20
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1723
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 146
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12551
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1562
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 31532
  bin: 7.5e0
  variant carriers: 0
hgvs: p.Pro232Ser
num of homozygotes: 0
population: Latino
population: European (Finnish)
population: European (Non-Finnish)
population: Other
population: African
population: East Asian
population: South Asian
reference allele: G
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: VQSLOD
site quality: MQ
site quality: ClippingRankSum
site quality: QD
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: DP
site quality: FS

9-139916048-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916048
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916048
    reference: chr 9
allele count: 9
allele frequency: 5.263157894736842e-4
allele num: 17100
alternate allele: G
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.693T>C
  hgvsp: ENST00000341511.6:c.693T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.780T>C
  hgvsp: ENST00000459850.1:c.780T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.693T>C
  hgvsp: ENST00000265662.5:c.693T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1587T>C
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.796T>C
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.780T>C
  hgvsp: ENST00000487109.1:c.780T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.737T>C
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.690T>C
  hgvsp: ENST00000371605.3:c.690T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 103
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32707
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 34
  bin: 4.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 6.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2261
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3158
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13726
  bin: 7.5e0
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 542
  bin: 3.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 173
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2392
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 7.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 48
  bin: 4.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 20
  bin: 5.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 29
  bin: 5.25e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 82
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 108
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 31944
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2085
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10202
  bin: 2.25e1
  variant carriers: 0
hgvs: p.Ala231Ala
num of homozygotes: 0
population: Latino
population: European (Finnish)
population: European (Non-Finnish)
population: African
population: East Asian
population: South Asian
population: Other
reference allele: A
site quality: InbreedingCoeff
site quality: FS
site quality: VQSLOD
site quality: MQ
site quality: MQRankSum
site quality: ClippingRankSum
site quality: ReadPosRankSum
site quality: BaseQRankSum
site quality: DP
site quality: QD

9-139916050-C-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916050
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916050
    reference: chr 9
allele count: 1
allele frequency: 5.861664712778429e-5
allele num: 17060
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.778G>C
  hgvsp: ENSP00000418662.1:p.Ala260Pro
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.688G>C
  hgvsp: ENSP00000360666.3:p.Ala230Pro
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.735G>C
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.691G>C
  hgvsp: ENSP00000344155.6:p.Ala231Pro
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.778G>C
  hgvsp: ENSP00000420527.1:p.Ala260Pro
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1585G>C
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.691G>C
  hgvsp: ENSP00000265662.5:p.Ala231Pro
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.794G>C
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 2340
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3153
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 159
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13720
  bin: 7.5e0
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 103
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32903
  bin: 2.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2271
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 22
  bin: 5.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 33
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 538
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 310
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 141
  bin: 9.75e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 1437
  bin: 1.25e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 53
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 215
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 32415
  bin: 7.5e0
  variant carriers: 0
hgvs: p.Ala231Pro
num of homozygotes: 0
population: European (Non-Finnish)
population: European (Finnish)
population: South Asian
population: Latino
population: East Asian
population: African
population: Other
reference allele: C
site quality: VQSLOD
site quality: QD
site quality: FS
site quality: ReadPosRankSum
site quality: MQ
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: MQRankSum
site quality: ClippingRankSum
site quality: DP

9-139916057-C-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916057
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916057
    reference: chr 9
allele count: 1
allele frequency: 6.195019204559534e-5
allele num: 16142
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.771G>C
  hgvsp: ENST00000459850.1:c.771G>C(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.771G>C
  hgvsp: ENST00000487109.1:c.771G>C(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.684G>C
  hgvsp: ENST00000341511.6:c.684G>C(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1578G>C
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.787G>C
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.684G>C
  hgvsp: ENST00000265662.5:c.684G>C(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.681G>C
  hgvsp: ENST00000371605.3:c.681G>C(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.728G>C
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 6.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 34373
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1938
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 531
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2249
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 102
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12089
  bin: 7.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 145
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3068
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 52
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 105
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1230
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 33912
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9830
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1345
  bin: 1.75e1
  variant carriers: 0
hgvs: p.Leu228Leu
num of homozygotes: 0
population: Latino
population: European (Finnish)
population: East Asian
population: African
population: South Asian
population: Other
population: European (Non-Finnish)
reference allele: C
site quality: VQSLOD
site quality: DP
site quality: MQRankSum
site quality: MQ
site quality: ReadPosRankSum
site quality: FS
site quality: QD
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: ClippingRankSum

9-139916067-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916067
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916067
    reference: chr 9
allele count: 1
allele frequency: 6.67913438418381e-5
allele num: 14972
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.676-5C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.782-5C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.766-5C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1568C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.723-5C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.679-5C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.679-5C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.766-5C>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: splice region
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 530
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2868
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 181
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9300
  bin: 7.5e0
  variant carriers: 4
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 103
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 35752
  bin: 2.5e0
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2170
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1582
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 50
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 53
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 30
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 296
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 92
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 18
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1168
  bin: 1.25e1
  variant carriers: 0
hgvs: c.679-5C>T
num of homozygotes: 0
population: Other
population: Latino
population: East Asian
population: African
population: South Asian
population: European (Non-Finnish)
population: European (Finnish)
reference allele: G
site quality: MQ
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: DP
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: FS
site quality: QD
site quality: BaseQRankSum
site quality: ClippingRankSum

9-139916087-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916087
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916087
    reference: chr 9
allele count: 0
allele frequency: 0.0e0
allele num: 13136
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.679-25C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.766-25C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.766-25C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.676-25C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.723-25C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1548C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.782-25C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.679-25C>T
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: 3' UTR
filter: AC_Adj0_Filter
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4996
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1842
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 19
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1863
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 724
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 34993
  bin: 2.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 93
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1618
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 360
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 73
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 306
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 698
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 138
  bin: 9.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 580
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 53
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4794
  bin: 2.5e0
  variant carriers: 0
num of homozygotes: 0
population: East Asian
population: European (Non-Finnish)
population: Latino
population: South Asian
population: African
population: Other
population: European (Finnish)
reference allele: G
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: QD
site quality: DP
site quality: FS
site quality: MQ

9-139916093-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916093
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916093
    reference: chr 9
allele count: 0
allele frequency: 0.0e0
allele num: 12846
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.723-31G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.782-31G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.766-31G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.679-31G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.766-31G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1542G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.679-31G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.676-31G>A
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: 3' UTR
filter: AC_Adj0_Filter
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 34223
  bin: 2.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 19
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4529
  bin: 7.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2010
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1504
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1279
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 88
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1212
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 280
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3008
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 609
  bin: 2.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 139
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 809
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 283
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 77
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2383
  bin: 6.25e1
  variant carriers: 0
num of homozygotes: 0
population: European (Finnish)
population: South Asian
population: European (Non-Finnish)
population: East Asian
population: Latino
population: African
population: Other
reference allele: C
site quality: QD
site quality: FS
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: DP
site quality: MQ
site quality: VQSLOD

9-139916100-GA-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916100
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916099
    reference: chr 9
allele count: 1
allele frequency: 7.923930269413629e-5
allele num: 12620
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.723-39delT
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.766-39delT
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.782-39delT
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.679-39delT
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.679-39delT
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.766-39delT
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1534delT
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.676-39delT
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: 3' UTR
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 45
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4347
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 197
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33488
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1759
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1986
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1260
  bin: 2.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 86
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 19
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 936
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 981
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 26794
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 225
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2767
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 45
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 239
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 60
  bin: 5.75e1
  variant carriers: 0
num of homozygotes: 0
population: South Asian
population: African
population: European (Finnish)
population: Latino
population: East Asian
population: Other
population: European (Non-Finnish)
reference allele: GA
site quality: BaseQRankSum
site quality: MQRankSum
site quality: ClippingRankSum
site quality: FS
site quality: QD
site quality: DP
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: MQ

9-139916114-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916114
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916114
    reference: chr 9
allele count: 1
allele frequency: 8.333333333333333e-5
allele num: 12000
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.782-52G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.723-52G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1521G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.679-52G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.766-52G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.676-52G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.766-52G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.679-52G>A
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: 3' UTR
filter: VQSRTrancheSNP99.60to99.80
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 639
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1381
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4534
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1861
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 32984
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1964
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 169
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 81
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 19
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 590
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 59
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21976
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11401
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 856
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 140
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 370
  bin: 4.25e1
  variant carriers: 0
num of homozygotes: 0
population: African
population: European (Non-Finnish)
population: Other
population: European (Finnish)
population: Latino
population: East Asian
population: South Asian
reference allele: C
site quality: DP
site quality: QD
site quality: ClippingRankSum
site quality: FS
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: BaseQRankSum
site quality: MQ
site quality: VQSLOD

9-139916310-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916310
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916310
    reference: chr 9
allele count: 1
allele frequency: 3.224558235521733e-5
allele num: 31012
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000476211
  gene symbol: ABCA2
  hgvsc: ENST00000476211.1:n.806G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1325G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.678+33G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.722+33G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.678+33G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000398207
  gene symbol: ABCA2
  hgvsc: ENST00000398207.4:n.799G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.765+33G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.675+33G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.765+33G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.781+33G>A
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: 3' UTR
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 5222
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1166
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 112
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1867
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 26163
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 139
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 229
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 793
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 78
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 66
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2069
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17609
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 712
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 319
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 161
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2081
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 449
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2101
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 14881
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 20831
  bin: 2.25e1
  variant carriers: 0
num of homozygotes: 0
population: European (Finnish)
population: African
population: Latino
population: East Asian
population: Other
population: South Asian
population: European (Non-Finnish)
reference allele: C
site quality: FS
site quality: QD
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: ReadPosRankSum
site quality: DP
site quality: MQ
site quality: MQRankSum
site quality: BaseQRankSum
site quality: ClippingRankSum

9-139916316-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916316
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916316
    reference: chr 9
allele count: 2
allele frequency: 6.233248145608676e-5
allele num: 32086
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.678+27C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000476211
  gene symbol: ABCA2
  hgvsc: ENST00000476211.1:n.800C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.675+27C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.765+27C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.765+27C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1319C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.781+27C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000398207
  gene symbol: ABCA2
  hgvsc: ENST00000398207.4:n.793C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.722+27C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.678+27C>T
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: 3' UTR
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 2143
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1930
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 646
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 78
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 803
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15468
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 319
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2315
  bin: 2.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 27870
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5488
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1170
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 161
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 66
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 449
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 229
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 112
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 139
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2735
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13587
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 905
  bin: 2.5e0
  variant carriers: 0
num of homozygotes: 0
population: East Asian
population: South Asian
population: Other
population: Latino
population: African
population: European (Non-Finnish)
population: European (Finnish)
reference allele: G
site quality: MQRankSum
site quality: BaseQRankSum
site quality: MQ
site quality: FS
site quality: InbreedingCoeff
site quality: DP
site quality: VQSLOD
site quality: ClippingRankSum
site quality: QD
site quality: ReadPosRankSum

http://identifiers.org/exac.variant/9-139916325-A-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916325
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916325
    reference: chr 9
allele count: 0
allele frequency: 0.0e0
allele num: 34458
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.722+18T>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1310T>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.678+18T>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.675+18T>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000476211
  gene symbol: ABCA2
  hgvsc: ENST00000476211.1:n.791T>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000398207
  gene symbol: ABCA2
  hgvsc: ENST00000398207.4:n.784T>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.765+18T>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.781+18T>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.678+18T>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.765+18T>G
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: 3' UTR
filter: AC_Adj0_Filter
genotype depth: GenotypeDepth
  all individuals: 139
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 78
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 321
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 161
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5837
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2249
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1192
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2017
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2817
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 30340
  bin: 7.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 66
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11998
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 814
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 231
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 112
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 723
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 454
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 202
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 119
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1966
  bin: 3.25e1
  variant carriers: 0
num of homozygotes: 0
population: European (Non-Finnish)
population: South Asian
population: European (Finnish)
population: African
population: East Asian
population: Latino
population: Other
reference allele: A
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: QD
site quality: MQ
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: FS
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: DP

9-139916326-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916326
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916326
    reference: chr 9
allele count: 1
allele frequency: 2.886669360891404e-5
allele num: 34642
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.781+17G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.678+17G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1309G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.765+17G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000398207
  gene symbol: ABCA2
  hgvsc: ENST00000398207.4:n.783G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.765+17G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000476211
  gene symbol: ABCA2
  hgvsc: ENST00000476211.1:n.790G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.722+17G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.678+17G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.675+17G>A
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: 3' UTR
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 815
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 321
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11661
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1196
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 733
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 161
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2259
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 78
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 455
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 66
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 30552
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5847
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2030
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2902
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 231
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 139
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 112
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1938
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 132
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 815
  bin: 3.75e1
  variant carriers: 0
num of homozygotes: 0
population: South Asian
population: European (Non-Finnish)
population: African
population: Other
population: Latino
population: East Asian
population: European (Finnish)
reference allele: C
site quality: VQSLOD
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: FS
site quality: InbreedingCoeff
site quality: MQ
site quality: BaseQRankSum
site quality: QD
site quality: DP
site quality: ClippingRankSum

http://identifiers.org/exac.variant/9-139916328-C-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916328
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916328
    reference: chr 9
allele count: 1
allele frequency: 2.850464625733995e-5
allele num: 35082
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.675+15G>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.781+15G>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.678+15G>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.678+15G>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1307G>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000398207
  gene symbol: ABCA2
  hgvsc: ENST00000398207.4:n.781G>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.722+15G>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.765+15G>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.765+15G>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000476211
  gene symbol: ABCA2
  hgvsc: ENST00000476211.1:n.788G>T
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: 3' UTR
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 139
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2035
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3088
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5826
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 31004
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10994
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 321
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1199
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 761
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 818
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 78
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 66
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 112
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 161
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 455
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2288
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 231
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 800
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 28353
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 715
  bin: 8.25e1
  variant carriers: 0
num of homozygotes: 0
population: East Asian
population: European (Non-Finnish)
population: African
population: European (Finnish)
population: Latino
population: Other
population: South Asian
reference allele: C
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: FS
site quality: QD
site quality: DP
site quality: MQ
site quality: BaseQRankSum

9-139916347-A-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916347
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916347
    reference: chr 9
allele count: 4
allele frequency: 9.284620026925398e-5
allele num: 43082
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.761T>A
  hgvsp: ENSP00000420527.1:p.Met254Lys
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.671T>A
  hgvsp: ENSP00000360666.3:p.Met224Lys
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000476211
  gene symbol: ABCA2
  hgvsc: ENST00000476211.1:n.769T>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1288T>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.674T>A
  hgvsp: ENSP00000344155.6:p.Met225Lys
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.718T>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.777T>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000398207
  gene symbol: ABCA2
  hgvsc: ENST00000398207.4:n.762T>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.674T>A
  hgvsp: ENSP00000265662.5:p.Met225Lys
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.761T>A
  hgvsp: ENSP00000418662.1:p.Met254Lys
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 5953
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1073
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 161
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 460
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32467
  bin: 7.5e0
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 140
  bin: 6.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2593
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 112
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1206
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5790
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2099
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 827
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 144
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6158
  bin: 2.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 232
  bin: 5.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 78
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 321
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 66
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1965
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 153
  bin: 5.75e1
  variant carriers: 0
hgvs: p.Met225Lys
num of homozygotes: 0
population: South Asian
population: Other
population: African
population: Latino
population: European (Non-Finnish)
population: European (Finnish)
population: East Asian
reference allele: A
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: DP
site quality: BaseQRankSum
site quality: VQSLOD
site quality: FS
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: MQ
site quality: QD

9-139916350-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916350
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916350
    reference: chr 9
allele count: 13
allele frequency: 2.92832364733973e-4
allele num: 44394
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.668G>A
  hgvsp: ENSP00000360666.3:p.Arg223Gln
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.758G>A
  hgvsp: ENSP00000418662.1:p.Arg253Gln
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1285G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000476211
  gene symbol: ABCA2
  hgvsc: ENST00000476211.1:n.766G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.774G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.758G>A
  hgvsp: ENSP00000420527.1:p.Arg253Gln
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.671G>A
  hgvsp: ENSP00000265662.5:p.Arg224Gln
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.671G>A
  hgvsp: ENSP00000344155.6:p.Arg224Gln
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.715G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000398207
  gene symbol: ABCA2
  hgvsc: ENST00000398207.4:n.759G>A
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 144
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 231
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5304
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1189
  bin: 1.75e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 2680
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 461
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 112
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1209
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5946
  bin: 1.25e1
  variant carriers: 5
genotype depth: GenotypeDepth
  all individuals: 827
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 79
  bin: 7.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 322
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32111
  bin: 7.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2130
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6793
  bin: 2.25e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 139
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 161
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 67
  bin: 8.25e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 400
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 242
  bin: 5.75e1
  variant carriers: 0
hgvs: p.Arg224Gln
num of homozygotes: 0
population: European (Finnish)
population: European (Non-Finnish)
population: African
population: South Asian
population: East Asian
population: Other
population: Latino
reference allele: C
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: FS
site quality: MQ
site quality: ClippingRankSum
site quality: VQSLOD
site quality: DP
site quality: QD

9-139916351-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916351
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916351
    reference: chr 9
allele count: 3
allele frequency: 6.648346777767928e-5
allele num: 45124
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1284C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.757C>T
  hgvsp: ENSP00000420527.1:p.Arg253Trp
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.670C>T
  hgvsp: ENSP00000265662.5:p.Arg224Trp
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.773C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.714C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.670C>T
  hgvsp: ENSP00000344155.6:p.Arg224Trp
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.667C>T
  hgvsp: ENSP00000360666.3:p.Arg223Trp
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.757C>T
  hgvsp: ENSP00000418662.1:p.Arg253Trp
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000476211
  gene symbol: ABCA2
  hgvsc: ENST00000476211.1:n.765C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000398207
  gene symbol: ABCA2
  hgvsc: ENST00000398207.4:n.758C>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 31944
  bin: 7.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 322
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5953
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 5084
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2706
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 144
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 827
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 112
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1210
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 232
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7070
  bin: 2.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 161
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2129
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1270
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 460
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 140
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 66
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 78
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4929
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1993
  bin: 6.75e1
  variant carriers: 0
hgvs: p.Arg224Trp
num of homozygotes: 0
population: African
population: European (Non-Finnish)
population: Latino
population: Other
population: South Asian
population: European (Finnish)
population: East Asian
reference allele: G
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: MQ
site quality: MQRankSum
site quality: VQSLOD
site quality: ReadPosRankSum
site quality: FS
site quality: DP
site quality: QD
site quality: InbreedingCoeff

9-139916365-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916365
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916365
    reference: chr 9
allele count: 3
allele frequency: 5.761032377001959e-5
allele num: 52074
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.743G>A
  hgvsp: ENSP00000420527.1:p.Gly248Asp
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1270G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000476211
  gene symbol: ABCA2
  hgvsc: ENST00000476211.1:n.751G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.743G>A
  hgvsp: ENSP00000418662.1:p.Gly248Asp
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.656G>A
  hgvsp: ENSP00000344155.6:p.Gly219Asp
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.759G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000398207
  gene symbol: ABCA2
  hgvsc: ENST00000398207.4:n.744G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.653G>A
  hgvsp: ENSP00000360666.3:p.Gly218Asp
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.656G>A
  hgvsp: ENSP00000265662.5:p.Gly219Asp
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.700G>A
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 5740
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 161
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3126
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 66
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29782
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 827
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3538
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 232
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1578
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 10239
  bin: 2.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2185
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 140
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1216
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 460
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 322
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 144
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 78
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 112
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1602
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 858
  bin: 3.75e1
  variant carriers: 0
hgvs: p.Gly219Asp
num of homozygotes: 0
population: Other
population: South Asian
population: East Asian
population: European (Non-Finnish)
population: Latino
population: African
population: European (Finnish)
reference allele: C
site quality: ReadPosRankSum
site quality: MQ
site quality: ClippingRankSum
site quality: DP
site quality: VQSLOD
site quality: BaseQRankSum
site quality: FS
site quality: MQRankSum
site quality: QD
site quality: InbreedingCoeff

9-139916368-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916368
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916368
    reference: chr 9
allele count: 1
allele frequency: 1.845018450184502e-5
allele num: 54200
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.740G>A
  hgvsp: ENSP00000420527.1:p.Gly247Glu
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.653G>A
  hgvsp: ENSP00000344155.6:p.Gly218Glu
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.756G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000398207
  gene symbol: ABCA2
  hgvsc: ENST00000398207.4:n.741G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.697G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.740G>A
  hgvsp: ENSP00000418662.1:p.Gly247Glu
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000476211
  gene symbol: ABCA2
  hgvsc: ENST00000476211.1:n.748G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.650G>A
  hgvsp: ENSP00000360666.3:p.Gly217Glu
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.653G>A
  hgvsp: ENSP00000265662.5:p.Gly218Glu
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1267G>A
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 2187
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1488
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 460
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29456
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 232
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 140
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 322
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 66
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 827
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1212
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5637
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3290
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 162
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3252
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 112
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 78
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10888
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1165
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 854
  bin: 3.75e1
  variant carriers: 0
hgvs: p.Gly218Glu
num of homozygotes: 0
population: European (Finnish)
population: East Asian
population: African
population: European (Non-Finnish)
population: Other
population: Latino
population: South Asian
reference allele: C
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: BaseQRankSum
site quality: FS
site quality: DP
site quality: VQSLOD
site quality: MQRankSum
site quality: QD
site quality: MQ

9-139916374-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916374
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916374
    reference: chr 9
allele count: 14
allele frequency: 2.464441627939727e-4
allele num: 56808
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.750G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.644G>A
  hgvsp: ENSP00000360666.3:p.Arg215His
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1261G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000476211
  gene symbol: ABCA2
  hgvsc: ENST00000476211.1:n.742G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.734G>A
  hgvsp: ENSP00000420527.1:p.Arg245His
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000398207
  gene symbol: ABCA2
  hgvsc: ENST00000398207.4:n.735G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.647G>A
  hgvsp: ENSP00000344155.6:p.Arg216His
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.647G>A
  hgvsp: ENSP00000265662.5:p.Arg216His
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.734G>A
  hgvsp: ENSP00000418662.1:p.Arg245His
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.691G>A
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 140
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2222
  bin: 3.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 828
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1213
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12176
  bin: 2.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2919
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 28333
  bin: 7.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 162
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 66
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1499
  bin: 1.75e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 3483
  bin: 2.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 322
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 78
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 232
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5560
  bin: 1.25e1
  variant carriers: 7
genotype depth: GenotypeDepth
  all individuals: 460
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 113
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 297
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13515
  bin: 6.25e1
  variant carriers: 0
hgvs: p.Arg216His
num of homozygotes: 0
population: East Asian
population: Latino
population: European (Non-Finnish)
population: South Asian
population: African
population: European (Finnish)
population: Other
reference allele: C
site quality: ClippingRankSum
site quality: ReadPosRankSum
site quality: BaseQRankSum
site quality: FS
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: DP
site quality: MQRankSum
site quality: MQ
site quality: QD

9-139916375-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916375
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916375
    reference: chr 9
allele count: 2
allele frequency: 3.484927687750479e-5
allele num: 57390
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.690C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.733C>T
  hgvsp: ENSP00000418662.1:p.Arg245Cys
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000398207
  gene symbol: ABCA2
  hgvsc: ENST00000398207.4:n.734C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1260C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.643C>T
  hgvsp: ENSP00000360666.3:p.Arg215Cys
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.733C>T
  hgvsp: ENSP00000420527.1:p.Arg245Cys
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.646C>T
  hgvsp: ENSP00000344155.6:p.Arg216Cys
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000476211
  gene symbol: ABCA2
  hgvsc: ENST00000476211.1:n.741C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.749C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.646C>T
  hgvsp: ENSP00000265662.5:p.Arg216Cys
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1212
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2875
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 460
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 232
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12177
  bin: 2.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 78
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 161
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1545
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 66
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2214
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 28212
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 140
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5608
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 113
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 828
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3563
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 323
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2244
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1523
  bin: 2.75e1
  variant carriers: 0
hgvs: p.Arg216Cys
num of homozygotes: 0
population: Other
population: European (Finnish)
population: East Asian
population: South Asian
population: African
population: Latino
population: European (Non-Finnish)
reference allele: G
site quality: FS
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: DP
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: ClippingRankSum
site quality: MQ
site quality: BaseQRankSum
site quality: QD

9-139916378-T-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916378
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916378
    reference: chr 9
allele count: 1
allele frequency: 1.693250702699042e-5
allele num: 59058
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.730A>G
  hgvsp: ENSP00000418662.1:p.Ser244Gly
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.730A>G
  hgvsp: ENSP00000420527.1:p.Ser244Gly
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.640A>G
  hgvsp: ENSP00000360666.3:p.Ser214Gly
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000398207
  gene symbol: ABCA2
  hgvsc: ENST00000398207.4:n.731A>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.643A>G
  hgvsp: ENSP00000265662.5:p.Ser215Gly
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1257A>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.687A>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000476211
  gene symbol: ABCA2
  hgvsc: ENST00000476211.1:n.738A>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.643A>G
  hgvsp: ENSP00000344155.6:p.Ser215Gly
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.746A>G
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1444
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5503
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2221
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 140
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 78
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1212
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3656
  bin: 2.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 66
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13021
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 27686
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2681
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 460
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 161
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 826
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 232
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 113
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 323
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 737
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1370
  bin: 3.25e1
  variant carriers: 0
hgvs: p.Ser215Gly
num of homozygotes: 0
population: African
population: Other
population: European (Non-Finnish)
population: East Asian
population: Latino
population: South Asian
population: European (Finnish)
reference allele: T
site quality: QD
site quality: ReadPosRankSum
site quality: BaseQRankSum
site quality: VQSLOD
site quality: DP
site quality: FS
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: MQ
site quality: ClippingRankSum

9-139916388-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916388
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916388
    reference: chr 9
allele count: 1
allele frequency: 1.589269253997012e-5
allele num: 62922
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.630G>A
  hgvsp: ENST00000371605.3:c.630G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000476211
  gene symbol: ABCA2
  hgvsc: ENST00000476211.1:n.728G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.720G>A
  hgvsp: ENST00000487109.1:c.720G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000398207
  gene symbol: ABCA2
  hgvsc: ENST00000398207.4:n.721G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1247G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.633G>A
  hgvsp: ENST00000265662.5:c.633G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.720G>A
  hgvsp: ENST00000459850.1:c.720G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.736G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.633G>A
  hgvsp: ENST00000341511.6:c.633G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.677G>A
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14517
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5616
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1411
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 78
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 26039
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 161
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 460
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 826
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2248
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2388
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 113
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 140
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4005
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 232
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 66
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1215
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 323
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 164
  bin: 2.5e0
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 2396
  bin: 7.5e0
  variant carriers: 0
hgvs: p.Gln211Gln
num of homozygotes: 0
population: European (Finnish)
population: East Asian
population: African
population: Latino
population: Other
population: South Asian
population: European (Non-Finnish)
reference allele: C
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: MQ
site quality: VQSLOD
site quality: FS
site quality: DP
site quality: QD
site quality: MQRankSum
site quality: ClippingRankSum

9-139916390-G-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916390
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916390
    reference: chr 9
allele count: 2
allele frequency: 3.165157941381275e-5
allele num: 63188
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.628C>A
  hgvsp: ENSP00000360666.3:p.Gln210Lys
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.675C>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000398207
  gene symbol: ABCA2
  hgvsc: ENST00000398207.4:n.719C>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.734C>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000476211
  gene symbol: ABCA2
  hgvsc: ENST00000476211.1:n.726C>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1245C>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.631C>A
  hgvsp: ENSP00000265662.5:p.Gln211Lys
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.718C>A
  hgvsp: ENSP00000420527.1:p.Gln240Lys
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.631C>A
  hgvsp: ENSP00000344155.6:p.Gln211Lys
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.718C>A
  hgvsp: ENSP00000418662.1:p.Gln240Lys
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 5855
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 25821
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1499
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2260
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 140
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 323
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4049
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1214
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 113
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 460
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 161
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14332
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2410
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 826
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 232
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 66
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 78
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2451
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 27894
  bin: 2.25e1
  variant carriers: 0
hgvs: p.Gln211Lys
num of homozygotes: 0
population: South Asian
population: East Asian
population: Latino
population: European (Finnish)
population: African
population: Other
population: European (Non-Finnish)
reference allele: G
site quality: InbreedingCoeff
site quality: DP
site quality: MQ
site quality: FS
site quality: MQRankSum
site quality: VQSLOD
site quality: ReadPosRankSum
site quality: QD
site quality: ClippingRankSum
site quality: BaseQRankSum

9-139916399-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916399
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916399
    reference: chr 9
allele count: 1
allele frequency: 1.539645881447267e-5
allele num: 64950
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.709C>T
  hgvsp: ENSP00000420527.1:p.His237Tyr
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.622C>T
  hgvsp: ENSP00000344155.6:p.His208Tyr
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.619C>T
  hgvsp: ENSP00000360666.3:p.His207Tyr
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.709C>T
  hgvsp: ENSP00000418662.1:p.His237Tyr
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.622C>T
  hgvsp: ENSP00000265662.5:p.His208Tyr
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1236C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000476211
  gene symbol: ABCA2
  hgvsc: ENST00000476211.1:n.717C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.666C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000398207
  gene symbol: ABCA2
  hgvsc: ENST00000398207.4:n.710C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.725C>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: VQSRTrancheSNP99.60to99.80
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2271
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6365
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1219
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1404
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 24977
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 460
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 66
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2410
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 78
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4216
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14576
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 323
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 826
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 161
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 113
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 140
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 232
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 662
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 610
  bin: 3.75e1
  variant carriers: 0
hgvs: p.His208Tyr
num of homozygotes: 0
population: European (Finnish)
population: African
population: East Asian
population: Latino
population: European (Non-Finnish)
population: Other
population: South Asian
reference allele: G
site quality: MQRankSum
site quality: FS
site quality: ReadPosRankSum
site quality: ClippingRankSum
site quality: MQ
site quality: VQSLOD
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: QD
site quality: DP

9-139916404-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916404
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916404
    reference: chr 9
allele count: 7
allele frequency: 1.07197549770291e-4
allele num: 65300
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.617G>A
  hgvsp: ENSP00000265662.5:p.Gly206Asp
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.661G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.720G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.617G>A
  hgvsp: ENSP00000344155.6:p.Gly206Asp
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.704G>A
  hgvsp: ENSP00000418662.1:p.Gly235Asp
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.614G>A
  hgvsp: ENSP00000360666.3:p.Gly205Asp
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000398207
  gene symbol: ABCA2
  hgvsc: ENST00000398207.4:n.705G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.704G>A
  hgvsp: ENSP00000420527.1:p.Gly235Asp
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000476211
  gene symbol: ABCA2
  hgvsc: ENST00000476211.1:n.712G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1231G>A
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1217
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1456
  bin: 1.75e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 827
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 323
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 161
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2275
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7099
  bin: 1.25e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 2522
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4255
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13926
  bin: 2.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 140
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 24673
  bin: 7.5e0
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 66
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 113
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 78
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 232
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 460
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2583
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1114
  bin: 9.75e1
  variant carriers: 8
hgvs: p.Gly206Asp
num of homozygotes: 0
population: East Asian
population: Latino
population: Other
population: African
population: European (Finnish)
population: European (Non-Finnish)
population: South Asian
reference allele: C
site quality: DP
site quality: FS
site quality: MQRankSum
site quality: MQ
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: QD
site quality: ReadPosRankSum
site quality: ClippingRankSum

9-139916411-G-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916411
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916411
    reference: chr 9
allele count: 1
allele frequency: 1.536334306345061e-5
allele num: 65090
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.697C>G
  hgvsp: ENSP00000420527.1:p.Gln233Glu
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.610C>G
  hgvsp: ENSP00000265662.5:p.Gln204Glu
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1224C>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000476211
  gene symbol: ABCA2
  hgvsc: ENST00000476211.1:n.705C>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.713C>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.697C>G
  hgvsp: ENSP00000418662.1:p.Gln233Glu
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.610C>G
  hgvsp: ENSP00000344155.6:p.Gln204Glu
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.607C>G
  hgvsp: ENSP00000360666.3:p.Gln203Glu
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.654C>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000398207
  gene symbol: ABCA2
  hgvsc: ENST00000398207.4:n.698C>G
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 140
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4238
  bin: 2.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 827
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 66
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 24345
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12368
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1541
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2922
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8505
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 323
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 460
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 113
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 232
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2266
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1215
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 78
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 161
  bin: 9.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 144
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 301
  bin: 4.75e1
  variant carriers: 0
hgvs: p.Gln204Glu
num of homozygotes: 0
population: African
population: European (Non-Finnish)
population: South Asian
population: East Asian
population: Latino
population: European (Finnish)
population: Other
reference allele: G
site quality: BaseQRankSum
site quality: DP
site quality: VQSLOD
site quality: MQRankSum
site quality: MQ
site quality: QD
site quality: FS
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: ReadPosRankSum

9-139916420-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916420
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916420
    reference: chr 9
allele count: 2
allele frequency: 3.127443315089914e-5
allele num: 63950
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1215C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.598C>T
  hgvsp: ENST00000371605.3:c.598C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000398207
  gene symbol: ABCA2
  hgvsc: ENST00000398207.4:n.689C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.601C>T
  hgvsp: ENST00000341511.6:c.601C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.704C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000476211
  gene symbol: ABCA2
  hgvsc: ENST00000476211.1:n.696C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.688C>T
  hgvsp: ENST00000459850.1:c.688C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.601C>T
  hgvsp: ENST00000265662.5:c.601C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.645C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.688C>T
  hgvsp: ENST00000487109.1:c.688C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 323
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1215
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4076
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2257
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 140
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 232
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4031
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 66
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2200
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 161
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 830
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 460
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8919
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11060
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 23583
  bin: 7.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 114
  bin: 7.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 78
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2182
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 440
  bin: 1.25e1
  variant carriers: 0
hgvs: p.Leu201Leu
num of homozygotes: 0
population: Latino
population: European (Finnish)
population: European (Non-Finnish)
population: African
population: South Asian
population: East Asian
population: Other
reference allele: G
site quality: FS
site quality: QD
site quality: InbreedingCoeff
site quality: MQ
site quality: BaseQRankSum
site quality: MQRankSum
site quality: VQSLOD
site quality: ClippingRankSum
site quality: DP
site quality: ReadPosRankSum

9-139916430-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916430
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916430
    reference: chr 9
allele count: 13
allele frequency: 2.071119041549834e-4
allele num: 62768
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.635C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.591C>T
  hgvsp: ENST00000341511.6:c.591C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.588C>T
  hgvsp: ENST00000371605.3:c.588C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1205C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000398207
  gene symbol: ABCA2
  hgvsc: ENST00000398207.4:n.679C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000476211
  gene symbol: ABCA2
  hgvsc: ENST00000476211.1:n.686C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.591C>T
  hgvsp: ENST00000265662.5:c.591C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.678C>T
  hgvsp: ENST00000487109.1:c.678C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.694C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.678C>T
  hgvsp: ENST00000459850.1:c.678C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 78
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 234
  bin: 5.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 22589
  bin: 7.5e0
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 3644
  bin: 2.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 324
  bin: 5.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 12876
  bin: 1.25e1
  variant carriers: 4
genotype depth: GenotypeDepth
  all individuals: 142
  bin: 6.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2783
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5424
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 66
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1219
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 835
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 463
  bin: 4.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 6457
  bin: 2.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 163
  bin: 9.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 113
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2268
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2054
  bin: 2.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 892
  bin: 3.75e1
  variant carriers: 0
hgvs: p.Pro197Pro
num of homozygotes: 0
population: African
population: Other
population: European (Non-Finnish)
population: European (Finnish)
population: South Asian
population: East Asian
population: Latino
reference allele: G
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: DP
site quality: FS
site quality: MQRankSum
site quality: MQ
site quality: QD

9-139916431-G-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916431
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916431
    reference: chr 9
allele count: 3
allele frequency: 4.797236791608034e-5
allele num: 62536
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.590C>G
  hgvsp: ENSP00000265662.5:p.Pro197Arg
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.587C>G
  hgvsp: ENSP00000360666.3:p.Pro196Arg
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.677C>G
  hgvsp: ENSP00000418662.1:p.Pro226Arg
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.693C>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000476211
  gene symbol: ABCA2
  hgvsc: ENST00000476211.1:n.685C>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1204C>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.590C>G
  hgvsp: ENSP00000344155.6:p.Pro197Arg
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.677C>G
  hgvsp: ENSP00000420527.1:p.Pro226Arg
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000398207
  gene symbol: ABCA2
  hgvsc: ENST00000398207.4:n.678C>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.634C>G
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3541
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1220
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 233
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5736
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13283
  bin: 1.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 838
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 324
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 162
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2249
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3005
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5941
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 114
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 22249
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 66
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 463
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 141
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 78
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1112
  bin: 9.75e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 750
  bin: 1.25e1
  variant carriers: 0
hgvs: p.Pro197Arg
num of homozygotes: 0
population: African
population: Latino
population: East Asian
population: Other
population: South Asian
population: European (Non-Finnish)
population: European (Finnish)
reference allele: G
site quality: InbreedingCoeff
site quality: MQ
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: MQRankSum
site quality: FS
site quality: QD
site quality: DP
site quality: ClippingRankSum

9-139916432-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916432
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916432
    reference: chr 9
allele count: 1
allele frequency: 1.601486179174274e-5
allele num: 62442
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.633C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.676C>T
  hgvsp: ENSP00000420527.1:p.Pro226Ser
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.692C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000476211
  gene symbol: ABCA2
  hgvsc: ENST00000476211.1:n.684C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.589C>T
  hgvsp: ENSP00000265662.5:p.Pro197Ser
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1203C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.589C>T
  hgvsp: ENSP00000344155.6:p.Pro197Ser
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000398207
  gene symbol: ABCA2
  hgvsc: ENST00000398207.4:n.677C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.586C>T
  hgvsp: ENSP00000360666.3:p.Pro196Ser
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.676C>T
  hgvsp: ENSP00000418662.1:p.Pro226Ser
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 78
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2259
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1220
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2988
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 462
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 141
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 838
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 115
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 66
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5709
  bin: 2.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3534
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 323
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5977
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 161
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 22190
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13347
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 233
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 770
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 619
  bin: 1.75e1
  variant carriers: 0
hgvs: p.Pro197Ser
num of homozygotes: 0
population: Latino
population: European (Finnish)
population: European (Non-Finnish)
population: African
population: East Asian
population: South Asian
population: Other
reference allele: G
site quality: FS
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: DP
site quality: MQRankSum
site quality: ClippingRankSum
site quality: ReadPosRankSum
site quality: MQ
site quality: VQSLOD
site quality: QD

9-139916433-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916433
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916433
    reference: chr 9
allele count: 1
allele frequency: 1.61311136920893e-5
allele num: 61992
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.585T>C
  hgvsp: ENST00000371605.3:c.585T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.691T>C
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1202T>C
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.588T>C
  hgvsp: ENST00000265662.5:c.588T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.588T>C
  hgvsp: ENST00000341511.6:c.588T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000476211
  gene symbol: ABCA2
  hgvsc: ENST00000476211.1:n.683T>C
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000398207
  gene symbol: ABCA2
  hgvsc: ENST00000398207.4:n.676T>C
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.675T>C
  hgvsp: ENST00000459850.1:c.675T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.632T>C
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.675T>C
  hgvsp: ENST00000487109.1:c.675T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 3255
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 461
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 323
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1225
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13616
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6571
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2254
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 115
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 141
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3414
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 21750
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 161
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5099
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 834
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 143
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 66
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 233
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 78
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 978
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 30254
  bin: 2.25e1
  variant carriers: 0
hgvs: p.Gly196Gly
num of homozygotes: 0
population: African
population: European (Non-Finnish)
population: Other
population: East Asian
population: Latino
population: European (Finnish)
population: South Asian
reference allele: A
site quality: ReadPosRankSum
site quality: DP
site quality: BaseQRankSum
site quality: FS
site quality: VQSLOD
site quality: MQ
site quality: QD
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: ClippingRankSum

9-139916461-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916461
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916461
    reference: chr 9
allele count: 1
allele frequency: 5.878894767783657e-5
allele num: 17010
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000398207
  gene symbol: ABCA2
  hgvsc: ENST00000398207.4:n.656-8C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.568-8C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000476211
  gene symbol: ABCA2
  hgvsc: ENST00000476211.1:n.663-8C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1182-8C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.655-8C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.565-8C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.568-8C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.655-8C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.612-8C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.671-8C>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: splice region
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 924
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 551
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 966
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 854
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1016
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1038
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 355
  bin: 7.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2199
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 21703
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12065
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 172
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8472
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 975
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 990
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 437
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 96
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 223
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 92
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 314
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 940
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
hgvs: c.568-8C>T
num of homozygotes: 0
population: European (Finnish)
population: Latino
population: African
population: South Asian
population: European (Non-Finnish)
population: Other
population: East Asian
reference allele: G
site quality: QD
site quality: ReadPosRankSum
site quality: FS
site quality: MQRankSum
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: DP
site quality: ClippingRankSum
site quality: VQSLOD
site quality: MQ

9-139916463-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916463
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916463
    reference: chr 9
allele count: 1
allele frequency: 6.924248719013987e-5
allele num: 14442
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.671-10C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.612-10C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.568-10C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.655-10C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000476211
  gene symbol: ABCA2
  hgvsc: ENST00000476211.1:n.663-10C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.568-10C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000398207
  gene symbol: ABCA2
  hgvsc: ENST00000398207.4:n.656-10C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.565-10C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1182-10C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.655-10C>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 823
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1043
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 330
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 900
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 452
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2044
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 840
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1063
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 212
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1013
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1044
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 22110
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7856
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 156
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11373
  bin: 2.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 557
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 104
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 92
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 898
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 339
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 83
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 783
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3222
  bin: 1.25e1
  variant carriers: 0
num of homozygotes: 0
population: Latino
population: East Asian
population: European (Non-Finnish)
population: African
population: European (Finnish)
population: South Asian
population: Other
reference allele: G
site quality: ReadPosRankSum
site quality: ClippingRankSum
site quality: MQRankSum
site quality: FS
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: MQ
site quality: QD
site quality: DP

9-139916464-T-TGGGGGAATGGCTCAGATGGGGTGTG
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916464
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916489
    reference: chr 9
allele count: 16
allele frequency: 1.18150937823069e-3
allele num: 13542
alternate allele: TGGGGGAATGGCTCAGATGGGGTGTG
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000398207
  gene symbol: ABCA2
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000476211
  gene symbol: ABCA2
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: intron
filter: VQSRTrancheINDEL97.00to99.00
genotype depth: GenotypeDepth
  all individuals: 851
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1049
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 215
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1103
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 434
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 88
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 751
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 22227
  bin: 7.5e0
  variant carriers: 7
genotype depth: GenotypeDepth
  all individuals: 159
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 104
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11254
  bin: 2.5e0
  variant carriers: 5
genotype depth: GenotypeDepth
  all individuals: 1852
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 582
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 342
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1036
  bin: 5.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 7635
  bin: 1.25e1
  variant carriers: 4
genotype depth: GenotypeDepth
  all individuals: 1015
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 353
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 871
  bin: 3.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 818
  bin: 2.25e1
  variant carriers: 5
genotype quality: GenotypeQuality
  all individuals: 135
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 390
  bin: 6.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 114
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 556
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 741
  bin: 6.25e1
  variant carriers: 0
num of homozygotes: 2
population: Other
population: European (Non-Finnish)
population: African
population: European (Finnish)
population: South Asian
population: Latino
population: East Asian
reference allele: T
site quality: FS
site quality: MQRankSum
site quality: MQ
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: ClippingRankSum
site quality: DP
site quality: BaseQRankSum
site quality: QD

9-139916465-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139916465
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139916465
    reference: chr 9
allele count: 1
allele frequency: 3.232479958624256e-5
allele num: 30936
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000492260
  gene symbol: ABCA2
  hgvsc: ENST00000492260.1:n.671-12C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000476211
  gene symbol: ABCA2
  hgvsc: ENST00000476211.1:n.663-12C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.568-12C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000398207
  gene symbol: ABCA2
  hgvsc: ENST00000398207.4:n.656-12C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.655-12C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.655-12C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000417701
  ensembl transcript: ENST00000464876
  gene symbol: ABCA2
  hgvsc: ENST00000464876.1:c.*1182-12C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000494046
  gene symbol: ABCA2
  hgvsc: ENST00000494046.1:n.612-12C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.565-12C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.568-12C>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 823
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 923
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 310
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 22457
  bin: 7.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 782
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11403
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1076
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1033
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1778
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 778
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 99
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7522
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1111
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 200
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1097
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 140
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 441
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 328
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 83
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 542
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5721
  bin: 1.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 1125
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2268
  bin: 2.5e0
  variant carriers: 0
num of homozygotes: 0
population: African
reference allele: G

GenotypeQuality
all individuals: 899
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 789
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 401
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 102
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 67
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 306
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 6838
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1108
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 5216
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 143
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 82
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 330
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 862
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 228
bin: 9.75e1
variant carriers: 2

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 778
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5060
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 60878
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 15612
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8166
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 1.166861143523921e-4
allele num: 8570
num of homozygotes: 0

Latino
type: Population
allele count: 1
allele frequency: 9.240436148586214e-5
allele num: 10822
num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: 1.19e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: -5.27e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.8e-3

BaseQRankSum
type: SiteQuality
SIO_000300: -2.5e-2

MQ
type: SiteQuality
SIO_000300: 5.895e1

DP
type: SiteQuality
SIO_000300: 1.384606e6

QD
type: SiteQuality
SIO_000300: 9.289999999999999e0

MQRankSum
type: SiteQuality
SIO_000300: 2.8e-2

FS
type: SiteQuality
SIO_000300: 4.565e0

ClippingRankSum
type: SiteQuality
SIO_000300: -6.6e-2

GenotypeQuality
all individuals: 300
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1105
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 61
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 244
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 839
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 152
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 102
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 82
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 8320
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 706
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 312
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 975
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 874
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 225
bin: 9.75e1
variant carriers: 1

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 59894
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8034
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 15390
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 768
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 4904
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 1.19161105815062e-4
allele num: 8392
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10638
num of homozygotes: 0

ReadPosRankSum
type: SiteQuality
SIO_000300: 6.68e-1

MQRankSum
type: SiteQuality
SIO_000300: -1.6e-2

MQ
type: SiteQuality
SIO_000300: 6.0e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.5e-3

FS
type: SiteQuality
SIO_000300: 1.145e0

BaseQRankSum
type: SiteQuality
SIO_000300: -2.925e0

VQSLOD
type: SiteQuality
SIO_000300: 1.0e0

DP
type: SiteQuality
SIO_000300: 1.352032e6

ClippingRankSum
type: SiteQuality
SIO_000300: -1.383e0

QD
type: SiteQuality
SIO_000300: 1.099e1

GenotypeQuality
all individuals: 70
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 1120
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 81
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 9798
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 146
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 929
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 101
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 671
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 941
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 854
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1346
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 35849
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 225
bin: 9.75e1
variant carriers: 3

GenotypeQuality
all individuals: 4547
bin: 6.75e1
variant carriers: 0

European (Finnish)
type: Population
allele count: 1
allele frequency: 2.111486486486487e-4
allele num: 4736
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8162
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7822
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 762
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.701490505682978e-5
allele num: 58772
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 6.605892456070815e-5
allele num: 15138
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10416
num of homozygotes: 0

BaseQRankSum
type: SiteQuality
SIO_000300: -1.7e-1

MQ
type: SiteQuality
SIO_000300: 5.911e1

QD
type: SiteQuality
SIO_000300: 8.5e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.7e-3

MQRankSum
type: SiteQuality
SIO_000300: -3.97e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 8.3e-1

FS
type: SiteQuality
SIO_000300: 1.075e1

VQSLOD
type: SiteQuality
SIO_000300: -1.69e0

DP
type: SiteQuality
SIO_000300: 1.315936e6

ClippingRankSum
type: SiteQuality
SIO_000300: -6.23e-1

GenotypeQuality
all individuals: 4536
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1352
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 80
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 9866
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 223
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 403
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 711
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 845
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 350
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 928
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 98
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 288
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 842
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1002
bin: 7.25e1
variant carriers: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8160
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7818
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10422
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 762
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.700738120344229e-5
allele num: 58798
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 15136
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 4740
num of homozygotes: 0

ClippingRankSum
type: SiteQuality
SIO_000300: 1.96e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -5.89e-1

MQRankSum
type: SiteQuality
SIO_000300: -1.96e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.5e-3

MQ
type: SiteQuality
SIO_000300: 6.0e1

DP
type: SiteQuality
SIO_000300: 1.315145e6

ReadPosRankSum
type: SiteQuality
SIO_000300: -2.84e-1

FS
type: SiteQuality
SIO_000300: 1.55e0

VQSLOD
type: SiteQuality
SIO_000300: 8.47e-1

QD
type: SiteQuality
SIO_000300: 1.164e1

GenotypeQuality
all individuals: 871
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 35859
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 322
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 77
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 251
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 944
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1159
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 915
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 79
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 727
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 10183
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 288
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 4490
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 226
bin: 9.75e1
variant carriers: 5

South Asian
type: Population
allele count: 2
allele frequency: 1.324854266030737e-4
allele num: 15096
num of homozygotes: 0

East Asian
type: Population
allele count: 1
allele frequency: 1.286008230452675e-4
allele num: 7776
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 756
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 58506
num of homozygotes: 0

Latino
type: Population
allele count: 2
allele frequency: 1.930874686232864e-4
allele num: 10358
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8106
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 4700
num of homozygotes: 0

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.5e-3

FS
type: SiteQuality
SIO_000300: 4.908e0

VQSLOD
type: SiteQuality
SIO_000300: 9.29e-1

MQRankSum
type: SiteQuality
SIO_000300: 0.0e0

DP
type: SiteQuality
SIO_000300: 1.307265e6

ReadPosRankSum
type: SiteQuality
SIO_000300: -7.2e-1

MQ
type: SiteQuality
SIO_000300: 5.934e1

ClippingRankSum
type: SiteQuality
SIO_000300: 5.13e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 1.82e-1

QD
type: SiteQuality
SIO_000300: 1.131e1

GenotypeQuality
all individuals: 56
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 12310
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 695
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 271
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 218
bin: 9.75e1
variant carriers: 2

GenotypeQuality
all individuals: 1360
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 343
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 146
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1569
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 896
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 771
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 77
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1067
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 87
bin: 9.25e1
variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7540
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7848
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 2
allele frequency: 3.501155381275821e-5
allele num: 57124
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 4526
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 746
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10012
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 14804
num of homozygotes: 0

MQ
type: SiteQuality
SIO_000300: 6.0e1

ClippingRankSum
type: SiteQuality
SIO_000300: -2.07e-1

MQRankSum
type: SiteQuality
SIO_000300: 2.07e-1

FS
type: SiteQuality
SIO_000300: 5.417e0

VQSLOD
type: SiteQuality
SIO_000300: 8.169999999999999e-1

QD
type: SiteQuality
SIO_000300: 1.077e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.8e-3

BaseQRankSum
type: SiteQuality
SIO_000300: -4.61e-1

DP
type: SiteQuality
SIO_000300: 1.257528e6

ReadPosRankSum
type: SiteQuality
SIO_000300: 9.55e-1

GenotypeQuality
all individuals: 435
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 13745
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 71
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 598
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1030
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 219
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 737
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 217
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 1723
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 263
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 3688
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 84
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 852
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 321
bin: 5.75e1
variant carriers: 0

Latino
type: Population
allele count: 1
allele frequency: 1.023541453428864e-4
allele num: 9770
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 742
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7686
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 4390
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7364
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 56062
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 14592
num of homozygotes: 0

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.04e0

DP
type: SiteQuality
SIO_000300: 1.225857e6

QD
type: SiteQuality
SIO_000300: 1.169e1

VQSLOD
type: SiteQuality
SIO_000300: 9.29e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -4.91e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 8.49e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -3.0e-3

MQ
type: SiteQuality
SIO_000300: 6.0e1

MQRankSum
type: SiteQuality
SIO_000300: 8.01e-1

FS
type: SiteQuality
SIO_000300: 0.0e0

GenotypeQuality
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bin: 1.75e1
variant carriers: 4

GenotypeQuality
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bin: 8.75e1
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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bin: 2.75e1
variant carriers: 1

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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bin: 3.25e1
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GenotypeQuality
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variant carriers: 3

GenotypeQuality
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variant carriers: 13

GenotypeQuality
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bin: 9.75e1
variant carriers: 1920

East Asian
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allele count: 2
allele frequency: 3.118178983473651e-4
allele num: 6414
num of homozygotes: 0

African
type: Population
allele count: 27
allele frequency: 3.91758560650029e-3
allele num: 6892
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1429
allele frequency: 2.832732030289815e-2
allele num: 50446
num of homozygotes: 16

Other
type: Population
allele count: 15
allele frequency: 2.199413489736071e-2
allele num: 682
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 131
allele frequency: 3.400830737279335e-2
allele num: 3852
num of homozygotes: 1

South Asian
type: Population
allele count: 338
allele frequency: 2.452118398142774e-2
allele num: 13784
num of homozygotes: 7

Latino
type: Population
allele count: 92
allele frequency: 1.094456340709017e-2
allele num: 8406
num of homozygotes: 4

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.92e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -1.444e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.4e-2

VQSLOD
type: SiteQuality
SIO_000300: 5.65e0

FS
type: SiteQuality
SIO_000300: 0.0e0

DP
type: SiteQuality
SIO_000300: 1.112382e6

ClippingRankSum
type: SiteQuality
SIO_000300: -7.3e-2

MQRankSum
type: SiteQuality
SIO_000300: 1.41e-1

QD
type: SiteQuality
SIO_000300: 1.151e1

MQ
type: SiteQuality
SIO_000300: 6.0e1

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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bin: 8.75e1
variant carriers: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 3852
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8406
num of homozygotes: 0

East Asian
type: Population
allele count: 1
allele frequency: 1.559089491736826e-4
allele num: 6414
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 682
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 13784
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6892
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 50446
num of homozygotes: 0

DP
type: SiteQuality
SIO_000300: 1.112382e6

ClippingRankSum
type: SiteQuality
SIO_000300: -7.3e-2

MQRankSum
type: SiteQuality
SIO_000300: 1.41e-1

QD
type: SiteQuality
SIO_000300: 1.151e1

BaseQRankSum
type: SiteQuality
SIO_000300: -1.444e0

FS
type: SiteQuality
SIO_000300: 0.0e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.4e-2

VQSLOD
type: SiteQuality
SIO_000300: 5.65e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.92e-1

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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bin: 2.75e1
variant carriers: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6514
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 7.524454477050414e-5
allele num: 13290
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 47214
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 3538
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5984
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7686
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 644
num of homozygotes: 0

QD
type: SiteQuality
SIO_000300: 7.32e0

VQSLOD
type: SiteQuality
SIO_000300: -3.839e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -7.55e-1

FS
type: SiteQuality
SIO_000300: 2.304e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -5.1e-3

MQRankSum
type: SiteQuality
SIO_000300: 2.22e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 3.11e-1

DP
type: SiteQuality
SIO_000300: 1.002868e6

BaseQRankSum
type: SiteQuality
SIO_000300: 7.55e-1

MQ
type: SiteQuality
SIO_000300: 5.871e1

GenotypeQuality
all individuals: 616
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 2412
bin: 3.25e1
variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
all individuals: 37
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GenotypeQuality
all individuals: 118
bin: 8.25e1
variant carriers: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 3474
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6400
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 634
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 7.581501137225171e-5
allele num: 13190
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5848
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7520
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 46292
num of homozygotes: 0

MQRankSum
type: SiteQuality
SIO_000300: -1.79e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 7.22e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -5.9e-3

VQSLOD
type: SiteQuality
SIO_000300: 1.59e0

FS
type: SiteQuality
SIO_000300: 0.0e0

DP
type: SiteQuality
SIO_000300: 9.86504e5

BaseQRankSum
type: SiteQuality
SIO_000300: -9.69e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -9.5e-1

QD
type: SiteQuality
SIO_000300: 1.838e1

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
all individuals: 596
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GenotypeQuality
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variant carriers: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 3406
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 45614
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5794
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7376
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 618
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6314
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 7.630093087135663e-5
allele num: 13106
num of homozygotes: 0

BaseQRankSum
type: SiteQuality
SIO_000300: 7.27e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 1.2e0

VQSLOD
type: SiteQuality
SIO_000300: 6.36e-1

MQRankSum
type: SiteQuality
SIO_000300: -2.98e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -5.8e-3

FS
type: SiteQuality
SIO_000300: 2.001e0

DP
type: SiteQuality
SIO_000300: 9.72842e5

MQ
type: SiteQuality
SIO_000300: 6.0e1

QD
type: SiteQuality
SIO_000300: 1.14e1

ReadPosRankSum
type: SiteQuality
SIO_000300: -4.6e-1

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 146

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 1

GenotypeQuality
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bin: 7.75e1
variant carriers: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 3166
num of homozygotes: 0

Latino
type: Population
allele count: 2
allele frequency: 2.9708853238265e-4
allele num: 6732
num of homozygotes: 0

South Asian
type: Population
allele count: 148
allele frequency: 1.168667087807959e-2
allele num: 12664
num of homozygotes: 1

European (Non-Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 42944
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5356
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African
type: Population
allele count: 0
allele frequency: 0.0e0
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num of homozygotes: 0

Other
type: Population
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allele num: 588
num of homozygotes: 0

DP
type: SiteQuality
SIO_000300: 9.14214e5

VQSLOD
type: SiteQuality
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ClippingRankSum
type: SiteQuality
SIO_000300: -4.9e-2

QD
type: SiteQuality
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MQRankSum
type: SiteQuality
SIO_000300: 2.33e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 3.92e-1

FS
type: SiteQuality
SIO_000300: 0.0e0

BaseQRankSum
type: SiteQuality
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InbreedingCoeff
type: SiteQuality
SIO_000300: -7.1e-3

MQ
type: SiteQuality
SIO_000300: 6.0e1

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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bin: 2.75e1
variant carriers: 0

East Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 5196
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5820
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 2
allele frequency: 4.768717215069146e-5
allele num: 41940
num of homozygotes: 0

Latino
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allele count: 0
allele frequency: 0.0e0
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num of homozygotes: 0

Other
type: Population
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allele frequency: 0.0e0
allele num: 572
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 12444
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European (Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 3062
num of homozygotes: 0

ClippingRankSum
type: SiteQuality
SIO_000300: 4.95e-1

MQ
type: SiteQuality
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BaseQRankSum
type: SiteQuality
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MQRankSum
type: SiteQuality
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FS
type: SiteQuality
SIO_000300: 7.65e-1

QD
type: SiteQuality
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VQSLOD
type: SiteQuality
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InbreedingCoeff
type: SiteQuality
SIO_000300: -7.900000000000001e-3

DP
type: SiteQuality
SIO_000300: 8.85795e5

ReadPosRankSum
type: SiteQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
all individuals: 248
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variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5094
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2972
num of homozygotes: 0

European (Non-Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 41144
num of homozygotes: 0

African
type: Population
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allele frequency: 0.0e0
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South Asian
type: Population
allele count: 1
allele frequency: 8.124796880077999e-5
allele num: 12308
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6304
num of homozygotes: 0

Other
type: Population
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allele frequency: 0.0e0
allele num: 568
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BaseQRankSum
type: SiteQuality
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QD
type: SiteQuality
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MQRankSum
type: SiteQuality
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MQ
type: SiteQuality
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InbreedingCoeff
type: SiteQuality
SIO_000300: -8.1e-3

FS
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ClippingRankSum
type: SiteQuality
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DP
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ReadPosRankSum
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VQSLOD
type: SiteQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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bin: 9.75e1
variant carriers: 1

African
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allele count: 0
allele frequency: 0.0e0
allele num: 5448
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 2.587991718426501e-5
allele num: 38640
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 550
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 4704
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5862
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2756
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11960
num of homozygotes: 0

MQRankSum
type: SiteQuality
SIO_000300: 2.3e0

ClippingRankSum
type: SiteQuality
SIO_000300: -1.913e0

MQ
type: SiteQuality
SIO_000300: 5.924e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -9.5e-3

BaseQRankSum
type: SiteQuality
SIO_000300: -4.406e0

QD
type: SiteQuality
SIO_000300: 1.208e1

FS
type: SiteQuality
SIO_000300: 2.527e0

VQSLOD
type: SiteQuality
SIO_000300: -1.388e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 2.45e0

DP
type: SiteQuality
SIO_000300: 8.2539e5

GenotypeQuality
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bin: 5.25e1
variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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Other
type: Population
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allele frequency: 0.0e0
allele num: 490
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5154
num of homozygotes: 0

European (Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 2444
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 4944
num of homozygotes: 0

South Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 11444
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 4150
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 2.878857669276831e-5
allele num: 34736
num of homozygotes: 0

DP
type: SiteQuality
SIO_000300: 7.61587e5

FS
type: SiteQuality
SIO_000300: 4.343e0

VQSLOD
type: SiteQuality
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InbreedingCoeff
type: SiteQuality
SIO_000300: 1.15e-2

MQ
type: SiteQuality
SIO_000300: 6.051e1

MQRankSum
type: SiteQuality
SIO_000300: -8.57e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 5.19e0

ReadPosRankSum
type: SiteQuality
SIO_000300: -2.86e-1

ClippingRankSum
type: SiteQuality
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QD
type: SiteQuality
SIO_000300: 7.97e0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

East Asian
type: Population
allele count: 1
allele frequency: 2.770083102493075e-4
allele num: 3610
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 4428
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 30368
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 448
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2080
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 4436
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10842
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 0.0e0

MQ
type: SiteQuality
SIO_000300: 5.911e1

MQRankSum
type: SiteQuality
SIO_000300: -3.11e-1

BaseQRankSum
type: SiteQuality
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VQSLOD
type: SiteQuality
SIO_000300: 8.73e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.62e-2

ClippingRankSum
type: SiteQuality
SIO_000300: 7.27e-1

QD
type: SiteQuality
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DP
type: SiteQuality
SIO_000300: 6.94109e5

ReadPosRankSum
type: SiteQuality
SIO_000300: -3.11e-1

GenotypeQuality
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variant carriers: 2

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

European (Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 1586
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10232
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 25140
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2944
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 2.707092582566324e-4
allele num: 3694
num of homozygotes: 0

Latino
type: Population
allele count: 1
allele frequency: 2.865329512893983e-4
allele num: 3490
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 386
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MQRankSum
type: SiteQuality
SIO_000300: 3.77e-1

DP
type: SiteQuality
SIO_000300: 6.30229e5

BaseQRankSum
type: SiteQuality
SIO_000300: 1.66e0

QD
type: SiteQuality
SIO_000300: 1.081e1

ReadPosRankSum
type: SiteQuality
SIO_000300: -1.01e-1

VQSLOD
type: SiteQuality
SIO_000300: -1.487e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.3e-2

ClippingRankSum
type: SiteQuality
SIO_000300: -3.77e-1

MQ
type: SiteQuality
SIO_000300: 5.518e1

FS
type: SiteQuality
SIO_000300: 9.587e0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 2

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 3674
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 388
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East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2912
num of homozygotes: 0

Latino
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allele count: 0
allele frequency: 0.0e0
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num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
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num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1554
num of homozygotes: 0

European (Non-Finnish)
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allele count: 2
allele frequency: 7.998720204767237e-5
allele num: 25004
num of homozygotes: 0

MQ
type: SiteQuality
SIO_000300: 6.0e1

BaseQRankSum
type: SiteQuality
SIO_000300: -1.246e0

VQSLOD
type: SiteQuality
SIO_000300: 5.1e-2

DP
type: SiteQuality
SIO_000300: 6.28232e5

QD
type: SiteQuality
SIO_000300: 8.279999999999999e0

MQRankSum
type: SiteQuality
SIO_000300: -1.4e-2

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.3e-2

ClippingRankSum
type: SiteQuality
SIO_000300: -7.78e-1

FS
type: SiteQuality
SIO_000300: 1.972e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 6.840000000000001e-1

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10140
num of homozygotes: 0

European (Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 1532
num of homozygotes: 0

Latino
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allele frequency: 0.0e0
allele num: 3380
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
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Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 378
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African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 3612
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European (Non-Finnish)
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allele count: 1
allele frequency: 4.072656186364747e-5
allele num: 24554
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ReadPosRankSum
type: SiteQuality
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BaseQRankSum
type: SiteQuality
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ClippingRankSum
type: SiteQuality
SIO_000300: 9.1e-1

FS
type: SiteQuality
SIO_000300: 2.276e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.34e-2

QD
type: SiteQuality
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MQRankSum
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VQSLOD
type: SiteQuality
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MQ
type: SiteQuality
SIO_000300: 6.0e1

DP
type: SiteQuality
SIO_000300: 6.22864e5

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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South Asian
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allele frequency: 0.0e0
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num of homozygotes: 0

European (Non-Finnish)
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allele frequency: 0.0e0
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Latino
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allele num: 2696
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African
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European (Finnish)
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allele count: 0
allele frequency: 0.0e0
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Other
type: Population
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East Asian
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ReadPosRankSum
type: SiteQuality
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MQRankSum
type: SiteQuality
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FS
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QD
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VQSLOD
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InbreedingCoeff
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BaseQRankSum
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DP
type: SiteQuality
SIO_000300: 5.70952e5

MQ
type: SiteQuality
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ClippingRankSum
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SIO_000300: -1.134e0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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South Asian
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East Asian
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European (Finnish)
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European (Non-Finnish)
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African
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Other
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Latino
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VQSLOD
type: SiteQuality
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FS
type: SiteQuality
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BaseQRankSum
type: SiteQuality
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QD
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ClippingRankSum
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ReadPosRankSum
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MQRankSum
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MQ
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DP
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InbreedingCoeff
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

European (Finnish)
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East Asian
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African
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South Asian
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European (Non-Finnish)
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allele count: 9
allele frequency: 5.004448398576513e-4
allele num: 17984
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Latino
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Other
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InbreedingCoeff
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QD
type: SiteQuality
SIO_000300: 1.26e1

FS
type: SiteQuality
SIO_000300: 8.705e0

MQRankSum
type: SiteQuality
SIO_000300: -2.37e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 1.52e0

DP
type: SiteQuality
SIO_000300: 5.47799e5

ReadPosRankSum
type: SiteQuality
SIO_000300: 3.22e-1

VQSLOD
type: SiteQuality
SIO_000300: 4.69e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

ClippingRankSum
type: SiteQuality
SIO_000300: 3.22e-1

GenotypeQuality
all individuals: 5872
bin: 6.25e1
variant carriers: 1

GenotypeQuality
all individuals: 1257
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 927
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 160
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 69
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 55
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 16259
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 344
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 59
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 118
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 27924
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 21
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 2698
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 156
bin: 7.25e1
variant carriers: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 926
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2664
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9434
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 5.57911180540058e-5
allele num: 17924
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2302
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2120
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 296
num of homozygotes: 0

InbreedingCoeff
type: SiteQuality
SIO_000300: -3.48e-2

MQ
type: SiteQuality
SIO_000300: 6.0e1

BaseQRankSum
type: SiteQuality
SIO_000300: -2.358e0

VQSLOD
type: SiteQuality
SIO_000300: -5.513e-1

MQRankSum
type: SiteQuality
SIO_000300: 3.22e-1

DP
type: SiteQuality
SIO_000300: 5.45875e5

FS
type: SiteQuality
SIO_000300: 1.998e0

ReadPosRankSum
type: SiteQuality
SIO_000300: -1.221e0

QD
type: SiteQuality
SIO_000300: 1.396e1

ClippingRankSum
type: SiteQuality
SIO_000300: -7.41e-1

GenotypeQuality
all individuals: 1010
bin: 2.5e0
variant carriers: 1

GenotypeQuality
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bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 25814
bin: 2.25e1
variant carriers: 1

GenotypeQuality
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bin: 5.25e1
variant carriers: 1

GenotypeQuality
all individuals: 635
bin: 6.75e1
variant carriers: 2

GenotypeQuality
all individuals: 22
bin: 5.75e1
variant carriers: 2

GenotypeQuality
all individuals: 188
bin: 9.75e1
variant carriers: 51

GenotypeQuality
all individuals: 1088
bin: 2.75e1
variant carriers: 1

GenotypeQuality
all individuals: 757
bin: 3.25e1
variant carriers: 0

GenotypeQuality
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bin: 8.75e1
variant carriers: 5

GenotypeQuality
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variant carriers: 1

GenotypeQuality
all individuals: 116
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 5672
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 249
bin: 3.75e1
variant carriers: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 716
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1832
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 22
allele frequency: 1.418988648090815e-3
allele num: 15504
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1858
num of homozygotes: 0

South Asian
type: Population
allele count: 26
allele frequency: 2.850252137689103e-3
allele num: 9122
num of homozygotes: 0

Other
type: Population
allele count: 1
allele frequency: 3.597122302158274e-3
allele num: 278
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 4.314063848144953e-4
allele num: 2318
num of homozygotes: 0

MQ
type: SiteQuality
SIO_000300: 6.0e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -3.97e-2

ClippingRankSum
type: SiteQuality
SIO_000300: -4.6e-2

FS
type: SiteQuality
SIO_000300: 0.0e0

QD
type: SiteQuality
SIO_000300: 1.296e1

MQRankSum
type: SiteQuality
SIO_000300: 0.0e0

BaseQRankSum
type: SiteQuality
SIO_000300: 1.43e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 4.21e-1

DP
type: SiteQuality
SIO_000300: 5.17771e5

VQSLOD
type: SiteQuality
SIO_000300: 4.29e0

GenotypeQuality
all individuals: 31
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 22
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 49
bin: 4.25e1
variant carriers: 0

GenotypeQuality
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bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 5632
bin: 6.25e1
variant carriers: 0

GenotypeQuality
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bin: 8.25e1
variant carriers: 0

GenotypeQuality
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bin: 1.75e1
variant carriers: 0

GenotypeQuality
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bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 21
bin: 8.75e1
variant carriers: 0

GenotypeQuality
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bin: 7.25e1
variant carriers: 0

GenotypeQuality
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bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 27
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 25014
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 702
bin: 3.25e1
variant carriers: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 638
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 260
num of homozygotes: 0

South Asian
type: Population
allele count: 2
allele frequency: 2.224694104560623e-4
allele num: 8990
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2180
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 14712
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1746
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1750
num of homozygotes: 0

MQ
type: SiteQuality
SIO_000300: 6.0e1

FS
type: SiteQuality
SIO_000300: 3.323e0

QD
type: SiteQuality
SIO_000300: 1.304e1

DP
type: SiteQuality
SIO_000300: 5.06077e5

ReadPosRankSum
type: SiteQuality
SIO_000300: 4.06e-1

VQSLOD
type: SiteQuality
SIO_000300: 4.89e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 7.41e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -8.999999999999999e-3

MQRankSum
type: SiteQuality
SIO_000300: 1.51e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 3.34e-2

GenotypeQuality
all individuals: 5632
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 25014
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1026
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 22
bin: 5.75e1
variant carriers: 1

GenotypeQuality
all individuals: 27
bin: 9.25e1
variant carriers: 1

GenotypeQuality
all individuals: 154
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variant carriers: 0

GenotypeQuality
all individuals: 2515
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 996
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variant carriers: 0

GenotypeQuality
all individuals: 21
bin: 8.75e1
variant carriers: 1

GenotypeQuality
all individuals: 31
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 117
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variant carriers: 2

GenotypeQuality
all individuals: 60
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variant carriers: 0

GenotypeQuality
all individuals: 644
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 49
bin: 4.25e1
variant carriers: 2

European (Non-Finnish)
type: Population
allele count: 5
allele frequency: 3.398586188145732e-4
allele num: 14712
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8990
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1746
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 260
num of homozygotes: 0

Latino
type: Population
allele count: 4
allele frequency: 2.285714285714286e-3
allele num: 1750
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 4.587155963302753e-4
allele num: 2180
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 638
num of homozygotes: 0

QD
type: SiteQuality
SIO_000300: 1.304e1

FS
type: SiteQuality
SIO_000300: 3.323e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 4.06e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 3.34e-2

DP
type: SiteQuality
SIO_000300: 5.06077e5

MQ
type: SiteQuality
SIO_000300: 6.0e1

BaseQRankSum
type: SiteQuality
SIO_000300: 7.41e-1

MQRankSum
type: SiteQuality
SIO_000300: 1.51e-1

VQSLOD
type: SiteQuality
SIO_000300: 4.89e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -8.999999999999999e-3

GenotypeQuality
all individuals: 20608
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 20
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variant carriers: 0

GenotypeQuality
all individuals: 661
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variant carriers: 0

GenotypeQuality
all individuals: 40
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variant carriers: 0

GenotypeQuality
all individuals: 26
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variant carriers: 0

GenotypeQuality
all individuals: 57
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variant carriers: 0

GenotypeQuality
all individuals: 23864
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variant carriers: 0

GenotypeQuality
all individuals: 60
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variant carriers: 0

GenotypeQuality
all individuals: 5555
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1625
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variant carriers: 0

GenotypeQuality
all individuals: 641
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 31
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 138
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 155
bin: 7.25e1
variant carriers: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1622
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 1.120573733751681e-4
allele num: 8924
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 13914
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 258
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2064
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 562
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1660
num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: -3.599e-1

FS
type: SiteQuality
SIO_000300: 3.901e0

BaseQRankSum
type: SiteQuality
SIO_000300: -2.889e0

QD
type: SiteQuality
SIO_000300: 1.322e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -4.26e-2

MQ
type: SiteQuality
SIO_000300: 6.0e1

MQRankSum
type: SiteQuality
SIO_000300: 1.03e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 9.91e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -7.64e-1

DP
type: SiteQuality
SIO_000300: 4.9707e5

GenotypeQuality
all individuals: 22
bin: 8.75e1
variant carriers: 1

GenotypeQuality
all individuals: 34
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 593
bin: 6.75e1
variant carriers: 1

GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 3357
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 2124
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 113
bin: 7.75e1
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GenotypeQuality
all individuals: 100
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variant carriers: 0

GenotypeQuality
all individuals: 28489
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GenotypeQuality
all individuals: 13369
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 28
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variant carriers: 0

GenotypeQuality
all individuals: 22
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variant carriers: 0

GenotypeQuality
all individuals: 148
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1882
bin: 1.25e1
variant carriers: 0

South Asian
type: Population
allele count: 19
allele frequency: 2.300242130750605e-3
allele num: 8260
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 742
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8540
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1264
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 964
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 182
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 202
num of homozygotes: 0

MQ
type: SiteQuality
SIO_000300: 5.974e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 4.06e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -3.543e0

FS
type: SiteQuality
SIO_000300: 0.0e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -6.14e-2

MQRankSum
type: SiteQuality
SIO_000300: 4.06e-1

DP
type: SiteQuality
SIO_000300: 4.11587e5

ClippingRankSum
type: SiteQuality
SIO_000300: -3.58e-1

QD
type: SiteQuality
SIO_000300: 1.389e1

VQSLOD
type: SiteQuality
SIO_000300: 3.75e0

GenotypeQuality
all individuals: 94
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 16
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 23
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2599
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variant carriers: 0

GenotypeQuality
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bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1720
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 24
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variant carriers: 0

GenotypeQuality
all individuals: 28969
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GenotypeQuality
all individuals: 1780
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 139
bin: 9.75e1
variant carriers: 2

GenotypeQuality
all individuals: 148
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 23
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 24
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 507
bin: 2.75e1
variant carriers: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 208
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8610
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1266
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 744
num of homozygotes: 0

South Asian
type: Population
allele count: 2
allele frequency: 2.424830261881668e-4
allele num: 8248
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 180
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 980
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 9.24e-1

MQRankSum
type: SiteQuality
SIO_000300: 2.34e0

BaseQRankSum
type: SiteQuality
SIO_000300: 8.999999999999999e-3

ReadPosRankSum
type: SiteQuality
SIO_000300: -6.72e-1

MQ
type: SiteQuality
SIO_000300: 5.973e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -6.07e-2

DP
type: SiteQuality
SIO_000300: 4.09653e5

VQSLOD
type: SiteQuality
SIO_000300: -2.642e0

QD
type: SiteQuality
SIO_000300: 1.661e1

ClippingRankSum
type: SiteQuality
SIO_000300: 9.01e-1

GenotypeQuality
all individuals: 88
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 19
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 291
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 19
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 137
bin: 9.75e1
variant carriers: 0

GenotypeQuality
all individuals: 508
bin: 2.75e1
variant carriers: 1

GenotypeQuality
all individuals: 21
bin: 8.75e1
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GenotypeQuality
all individuals: 113
bin: 7.75e1
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GenotypeQuality
all individuals: 1744
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 593
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 8
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 21
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 5229
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 14608
bin: 2.25e1
variant carriers: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8620
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1276
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 212
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 976
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 740
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8254
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 180
num of homozygotes: 0

ReadPosRankSum
type: SiteQuality
SIO_000300: -7.27e-1

FS
type: SiteQuality
SIO_000300: 0.0e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

MQRankSum
type: SiteQuality
SIO_000300: 7.27e-1

DP
type: SiteQuality
SIO_000300: 4.09339e5

BaseQRankSum
type: SiteQuality
SIO_000300: -7.27e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -6.05e-2

ClippingRankSum
type: SiteQuality
SIO_000300: 7.27e-1

VQSLOD
type: SiteQuality
SIO_000300: -2.319e0

QD
type: SiteQuality
SIO_000300: 7.58e0

GenotypeQuality
all individuals: 14272
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 275
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 21
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 30026
bin: 7.5e0
variant carriers: 1

GenotypeQuality
all individuals: 1437
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 1820
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 16
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 148
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 24
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 137
bin: 9.75e1
variant carriers: 0

GenotypeQuality
all individuals: 591
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 18
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 113
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 9
bin: 5.25e1
variant carriers: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 698
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 202
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 170
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8220
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1224
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 910
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8344
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 0.0e0

QD
type: SiteQuality
SIO_000300: 1.411e1

VQSLOD
type: SiteQuality
SIO_000300: 3.63e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -6.16e-2

DP
type: SiteQuality
SIO_000300: 4.02409e5

MQ
type: SiteQuality
SIO_000300: 6.0e1

GenotypeQuality
all individuals: 2501
bin: 1.75e1
variant carriers: 0

GenotypeQuality
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bin: 3.25e1
variant carriers: 0

GenotypeQuality
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bin: 7.75e1
variant carriers: 0

GenotypeQuality
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bin: 2.75e1
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GenotypeQuality
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bin: 4.75e1
variant carriers: 0

GenotypeQuality
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bin: 1.25e1
variant carriers: 0

GenotypeQuality
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bin: 7.25e1
variant carriers: 0

GenotypeQuality
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bin: 9.25e1
variant carriers: 0

GenotypeQuality
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bin: 6.75e1
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GenotypeQuality
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bin: 5.25e1
variant carriers: 0

GenotypeQuality
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bin: 9.75e1
variant carriers: 1

GenotypeQuality
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bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 56
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 21
bin: 8.75e1
variant carriers: 0

East Asian
type: Population
allele count: 1
allele frequency: 1.298701298701299e-3
allele num: 770
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8062
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7088
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1062
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 162
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 542
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 142
num of homozygotes: 0

ClippingRankSum
type: SiteQuality
SIO_000300: 1.77e0

VQSLOD
type: SiteQuality
SIO_000300: -3.917e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

MQRankSum
type: SiteQuality
SIO_000300: -6.94e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -1.774e0

ReadPosRankSum
type: SiteQuality
SIO_000300: -1.62e0

DP
type: SiteQuality
SIO_000300: 3.83872e5

InbreedingCoeff
type: SiteQuality
SIO_000300: -6.78e-2

FS
type: SiteQuality
SIO_000300: 0.0e0

QD
type: SiteQuality
SIO_000300: 3.43e0

GenotypeQuality
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bin: 6.25e1
variant carriers: 0

GenotypeQuality
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bin: 2.75e1
variant carriers: 0

GenotypeQuality
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variant carriers: 2

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 578
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variant carriers: 0

GenotypeQuality
all individuals: 109
bin: 7.75e1
variant carriers: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 552
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 148
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7324
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 162
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1116
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 774
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 1.238236750866766e-4
allele num: 8076
num of homozygotes: 0

ReadPosRankSum
type: SiteQuality
SIO_000300: 5.7e-2

MQRankSum
type: SiteQuality
SIO_000300: 2.03e0

VQSLOD
type: SiteQuality
SIO_000300: -1.978e0

MQ
type: SiteQuality
SIO_000300: 5.952e1

ClippingRankSum
type: SiteQuality
SIO_000300: 0.0e0

QD
type: SiteQuality
SIO_000300: 1.464e1

BaseQRankSum
type: SiteQuality
SIO_000300: -4.21e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -6.59e-2

DP
type: SiteQuality
SIO_000300: 3.84262e5

FS
type: SiteQuality
SIO_000300: 1.581e0

GenotypeQuality
all individuals: 18
bin: 8.75e1
variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 1

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 10

GenotypeQuality
all individuals: 569
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variant carriers: 0

GenotypeQuality
all individuals: 18
bin: 4.25e1
variant carriers: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 476
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 120
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 6
allele frequency: 9.036144578313253e-4
allele num: 6640
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1018
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 700
num of homozygotes: 0

South Asian
type: Population
allele count: 3
allele frequency: 3.756574004507889e-4
allele num: 7986
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 160
num of homozygotes: 0

InbreedingCoeff
type: SiteQuality
SIO_000300: -6.93e-2

FS
type: SiteQuality
SIO_000300: 0.0e0

VQSLOD
type: SiteQuality
SIO_000300: 3.22e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

MQRankSum
type: SiteQuality
SIO_000300: 0.0e0

ClippingRankSum
type: SiteQuality
SIO_000300: 0.0e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.06e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 3.65e-1

DP
type: SiteQuality
SIO_000300: 3.72282e5

QD
type: SiteQuality
SIO_000300: 1.391e1

GenotypeQuality
all individuals: 18
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 18
bin: 5.75e1
variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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variant carriers: 1

GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 107
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variant carriers: 0

GenotypeQuality
all individuals: 5081
bin: 6.25e1
variant carriers: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6606
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 126
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7968
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 480
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 692
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 9.727626459143969e-4
allele num: 1028
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 160
num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: 5.96e-1

QD
type: SiteQuality
SIO_000300: 8.92e0

FS
type: SiteQuality
SIO_000300: 0.0e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 7.31e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -6.87e-2

BaseQRankSum
type: SiteQuality
SIO_000300: 1.3e0

MQRankSum
type: SiteQuality
SIO_000300: 6.840000000000001e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 5.5e-1

DP
type: SiteQuality
SIO_000300: 3.72037e5

GenotypeQuality
all individuals: 19
bin: 4.25e1
variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 2

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
all individuals: 24
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GenotypeQuality
all individuals: 16
bin: 5.75e1
variant carriers: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 414
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 92
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 592
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 950
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7880
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 156
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.650709805216243e-4
allele num: 6058
num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: -5.404e-1

DP
type: SiteQuality
SIO_000300: 3.55843e5

MQRankSum
type: SiteQuality
SIO_000300: 2.33e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.31e0

FS
type: SiteQuality
SIO_000300: 0.0e0

QD
type: SiteQuality
SIO_000300: 1.56e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -7.190000000000001e-2

BaseQRankSum
type: SiteQuality
SIO_000300: -3.61e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -5.73e-1

GenotypeQuality
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bin: 1.75e1
variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 3

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
all individuals: 21
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GenotypeQuality
all individuals: 549
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variant carriers: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 154
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 322
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 516
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 848
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7696
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.864975755315181e-4
allele num: 5362
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 74
num of homozygotes: 0

MQ
type: SiteQuality
SIO_000300: 6.0e1

VQSLOD
type: SiteQuality
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InbreedingCoeff
type: SiteQuality
SIO_000300: -7.7e-2

DP
type: SiteQuality
SIO_000300: 3.27989e5

MQRankSum
type: SiteQuality
SIO_000300: 3.22e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 3.58e-1

FS
type: SiteQuality
SIO_000300: 6.591e0

QD
type: SiteQuality
SIO_000300: 1.028e1

BaseQRankSum
type: SiteQuality
SIO_000300: -7.27e-1

ClippingRankSum
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SIO_000300: 0.0e0

GenotypeQuality
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bin: 4.75e1
variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

East Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 376
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 4366
num of homozygotes: 0

Latino
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allele count: 0
allele frequency: 0.0e0
allele num: 234
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7286
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 698
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 142
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 34
num of homozygotes: 0

InbreedingCoeff
type: SiteQuality
SIO_000300: -8.67e-2

VQSLOD
type: SiteQuality
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QD
type: SiteQuality
SIO_000300: 1.53e1

DP
type: SiteQuality
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FS
type: SiteQuality
SIO_000300: 0.0e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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bin: 1.75e1
variant carriers: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 24
num of homozygotes: 0

South Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 7172
num of homozygotes: 0

European (Non-Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 4246
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 360
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 220
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African
type: Population
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allele frequency: 0.0e0
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num of homozygotes: 0

Other
type: Population
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allele num: 142
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QD
type: SiteQuality
SIO_000300: 8.5e0

FS
type: SiteQuality
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ReadPosRankSum
type: SiteQuality
SIO_000300: 7.27e-1

MQRankSum
type: SiteQuality
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InbreedingCoeff
type: SiteQuality
SIO_000300: -8.85e-2

BaseQRankSum
type: SiteQuality
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ClippingRankSum
type: SiteQuality
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DP
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MQ
type: SiteQuality
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VQSLOD
type: SiteQuality
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GenotypeQuality
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bin: 2.75e1
variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
all individuals: 65
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GenotypeQuality
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South Asian
type: Population
allele count: 1
allele frequency: 1.41282848262221e-4
allele num: 7078
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 662
num of homozygotes: 0

European (Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 26
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 208
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
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num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 140
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 4152
num of homozygotes: 0

BaseQRankSum
type: SiteQuality
SIO_000300: 1.23e0

MQRankSum
type: SiteQuality
SIO_000300: 5.43e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 3.6e-2

FS
type: SiteQuality
SIO_000300: 0.0e0

QD
type: SiteQuality
SIO_000300: 1.774e1

DP
type: SiteQuality
SIO_000300: 2.30695e5

VQSLOD
type: SiteQuality
SIO_000300: 3.28e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -9.02e-2

ReadPosRankSum
type: SiteQuality
SIO_000300: 7.27e-1

MQ
type: SiteQuality
SIO_000300: 6.051e1

GenotypeQuality
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bin: 3.25e1
variant carriers: 0

GenotypeQuality
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bin: 5.25e1
variant carriers: 0

GenotypeQuality
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bin: 6.75e1
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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bin: 1.75e1
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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bin: 5.75e1
variant carriers: 0

African
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allele count: 0
allele frequency: 0.0e0
allele num: 652
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 3940
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 134
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 26
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 206
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 344
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 1.492982979994028e-4
allele num: 6698
num of homozygotes: 0

DP
type: SiteQuality
SIO_000300: 2.27056e5

QD
type: SiteQuality
SIO_000300: 3.31e0

ClippingRankSum
type: SiteQuality
SIO_000300: 3.06e-1

FS
type: SiteQuality
SIO_000300: 0.0e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -9.9e-2

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.29e0

MQRankSum
type: SiteQuality
SIO_000300: -1.164e0

BaseQRankSum
type: SiteQuality
SIO_000300: -2.756e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

VQSLOD
type: SiteQuality
SIO_000300: -2.765e0

GenotypeQuality
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bin: 8.25e1
variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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bin: 6.25e1
variant carriers: 0

European (Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 382
num of homozygotes: 0

African
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allele count: 0
allele frequency: 0.0e0
allele num: 3298
num of homozygotes: 0

Latino
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allele count: 0
allele frequency: 0.0e0
allele num: 938
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
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num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 248
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 1.160631383472609e-4
allele num: 8616
num of homozygotes: 0

European (Non-Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 15394
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 0.0e0

QD
type: SiteQuality
SIO_000300: 1.195e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -3.01e-2

VQSLOD
type: SiteQuality
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ReadPosRankSum
type: SiteQuality
SIO_000300: -3.61e-1

DP
type: SiteQuality
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MQ
type: SiteQuality
SIO_000300: 6.0e1

MQRankSum
type: SiteQuality
SIO_000300: -1.93e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -2.219e0

ClippingRankSum
type: SiteQuality
SIO_000300: 1.22e0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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variant carriers: 0

East Asian
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allele count: 1
allele frequency: 4.401408450704225e-4
allele num: 2272
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8716
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 254
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 992
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 3448
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 6.264879087833605e-5
allele num: 15962
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 442
num of homozygotes: 0

MQRankSum
type: SiteQuality
SIO_000300: 6.8e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 0.0e0

MQ
type: SiteQuality
SIO_000300: 5.808e1

FS
type: SiteQuality
SIO_000300: 2.504e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.76e-2

DP
type: SiteQuality
SIO_000300: 6.81727e5

VQSLOD
type: SiteQuality
SIO_000300: -1.502e0

ClippingRankSum
type: SiteQuality
SIO_000300: 2.27e-1

QD
type: SiteQuality
SIO_000300: 8.08e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 7.22e-1

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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bin: 7.75e1
variant carriers: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 17386
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8896
num of homozygotes: 0

European (Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 514
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 3616
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2596
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1192
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 258
num of homozygotes: 0

ReadPosRankSum
type: SiteQuality
SIO_000300: -5.5e-1

VQSLOD
type: SiteQuality
SIO_000300: -1.437e0

QD
type: SiteQuality
SIO_000300: 1.044e1

MQ
type: SiteQuality
SIO_000300: 5.303e1

BaseQRankSum
type: SiteQuality
SIO_000300: 1.75e0

ClippingRankSum
type: SiteQuality
SIO_000300: -5.5e-1

FS
type: SiteQuality
SIO_000300: 3.68e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.29e-2

MQRankSum
type: SiteQuality
SIO_000300: 0.0e0

DP
type: SiteQuality
SIO_000300: 7.15516e5

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8918
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 17498
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 3632
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 262
num of homozygotes: 0

Latino
type: Population
allele count: 1
allele frequency: 8.278145695364238e-4
allele num: 1208
num of homozygotes: 0

East Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 2608
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 516
num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: -8.043e-1

MQRankSum
type: SiteQuality
SIO_000300: 5.36e-1

ReadPosRankSum
type: SiteQuality
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FS
type: SiteQuality
SIO_000300: 0.0e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.23e-2

MQ
type: SiteQuality
SIO_000300: 5.643e1

BaseQRankSum
type: SiteQuality
SIO_000300: -2.89e-1

QD
type: SiteQuality
SIO_000300: 1.334e1

DP
type: SiteQuality
SIO_000300: 7.19221e5

ClippingRankSum
type: SiteQuality
SIO_000300: -9.29e-1

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

East Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 2650
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
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num of homozygotes: 0

African
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allele count: 1
allele frequency: 2.701242571582928e-4
allele num: 3702
num of homozygotes: 0

European (Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 532
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1226
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 266
num of homozygotes: 0

South Asian
type: Population
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allele frequency: 0.0e0
allele num: 8948
num of homozygotes: 0

ClippingRankSum
type: SiteQuality
SIO_000300: 8.25e-1

InbreedingCoeff
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SIO_000300: -2.16e-2

MQRankSum
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SIO_000300: 1.7e0

ReadPosRankSum
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VQSLOD
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FS
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QD
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DP
type: SiteQuality
SIO_000300: 7.26324e5

MQ
type: SiteQuality
SIO_000300: 5.787e1

BaseQRankSum
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SIO_000300: 2.47e0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 1

South Asian
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Other
type: Population
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African
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allele frequency: 0.0e0
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Latino
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European (Non-Finnish)
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European (Finnish)
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East Asian
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allele frequency: 1.166180758017493e-3
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ReadPosRankSum
type: SiteQuality
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MQRankSum
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DP
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BaseQRankSum
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VQSLOD
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FS
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ClippingRankSum
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InbreedingCoeff
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MQ
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QD
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GenotypeQuality
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variant carriers: 1

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 12

European (Finnish)
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allele count: 0
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European (Non-Finnish)
type: Population
allele count: 5
allele frequency: 2.110060769750169e-4
allele num: 23696
num of homozygotes: 0

African
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South Asian
type: Population
allele count: 4
allele frequency: 4.192872117400419e-4
allele num: 9540
num of homozygotes: 0

East Asian
type: Population
allele count: 4
allele frequency: 1.131221719457014e-3
allele num: 3536
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 322
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1934
num of homozygotes: 0

MQRankSum
type: SiteQuality
SIO_000300: 2.12e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 3.2e-2

BaseQRankSum
type: SiteQuality
SIO_000300: -2.12e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.34e-2

FS
type: SiteQuality
SIO_000300: 6.21e-1

MQ
type: SiteQuality
SIO_000300: 5.481e1

ClippingRankSum
type: SiteQuality
SIO_000300: 7.27e-1

VQSLOD
type: SiteQuality
SIO_000300: -1.006e-1

DP
type: SiteQuality
SIO_000300: 8.2399e5

QD
type: SiteQuality
SIO_000300: 1.277e1

GenotypeQuality
all individuals: 415
bin: 5.25e1
variant carriers: 1

GenotypeQuality
all individuals: 1109
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 401
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 885
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variant carriers: 1

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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variant carriers: 1

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 380
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variant carriers: 0

GenotypeQuality
all individuals: 1811
bin: 3.25e1
variant carriers: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 4522
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 2
allele frequency: 8.279516476237788e-5
allele num: 24156
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1986
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 324
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 1.041016031646887e-4
allele num: 9606
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 3622
num of homozygotes: 0

ClippingRankSum
type: SiteQuality
SIO_000300: 4.46e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -9.55e-1

MQ
type: SiteQuality
SIO_000300: 5.705e1

MQRankSum
type: SiteQuality
SIO_000300: 3.49e-1

VQSLOD
type: SiteQuality
SIO_000300: -1.531e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 8.699999999999999e-2

FS
type: SiteQuality
SIO_000300: 0.0e0

DP
type: SiteQuality
SIO_000300: 8.30387e5

QD
type: SiteQuality
SIO_000300: 2.66e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.27e-2

GenotypeQuality
all individuals: 361
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1047
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
all individuals: 1082
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GenotypeQuality
all individuals: 2126
bin: 6.75e1
variant carriers: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 366
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 9.910802775024777e-5
allele num: 10090
num of homozygotes: 0

East Asian
type: Population
allele count: 1
allele frequency: 2.367424242424242e-4
allele num: 4224
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 3.493083694285315e-5
allele num: 28628
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2524
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5044
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1198
num of homozygotes: 0

ReadPosRankSum
type: SiteQuality
SIO_000300: -2.37e-1

MQ
type: SiteQuality
SIO_000300: 5.671e1

ClippingRankSum
type: SiteQuality
SIO_000300: 0.0e0

DP
type: SiteQuality
SIO_000300: 8.94925e5

VQSLOD
type: SiteQuality
SIO_000300: -1.674e0

BaseQRankSum
type: SiteQuality
SIO_000300: -1.354e0

FS
type: SiteQuality
SIO_000300: 6.408e0

MQRankSum
type: SiteQuality
SIO_000300: 1.31e0

QD
type: SiteQuality
SIO_000300: 3.64e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.12e-2

GenotypeQuality
all individuals: 1108
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 12098
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
all individuals: 1097
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 2183
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variant carriers: 0

GenotypeQuality
all individuals: 403
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 380
bin: 9.25e1
variant carriers: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1288
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 4342
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 1.925298421255295e-4
allele num: 5194
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 29964
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 376
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2782
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10254
num of homozygotes: 0

ClippingRankSum
type: SiteQuality
SIO_000300: 9.16e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -9.5e-3

ReadPosRankSum
type: SiteQuality
SIO_000300: 5.6e-2

BaseQRankSum
type: SiteQuality
SIO_000300: -4.44e-1

FS
type: SiteQuality
SIO_000300: 2.217e0

DP
type: SiteQuality
SIO_000300: 9.07112e5

VQSLOD
type: SiteQuality
SIO_000300: -1.586e0

MQRankSum
type: SiteQuality
SIO_000300: 1.24e0

QD
type: SiteQuality
SIO_000300: 2.464e1

MQ
type: SiteQuality
SIO_000300: 5.906e1

GenotypeQuality
all individuals: 1063
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1036
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 2891
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variant carriers: 0

GenotypeQuality
all individuals: 743
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variant carriers: 1

GenotypeQuality
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GenotypeQuality
all individuals: 404
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variant carriers: 0

GenotypeQuality
all individuals: 1520
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 792
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variant carriers: 0

GenotypeQuality
all individuals: 1436
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variant carriers: 0

GenotypeQuality
all individuals: 2245
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GenotypeQuality
all individuals: 561
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GenotypeQuality
all individuals: 546
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variant carriers: 0

GenotypeQuality
all individuals: 29192
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variant carriers: 0

GenotypeQuality
all individuals: 381
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GenotypeQuality
all individuals: 1116
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variant carriers: 10

GenotypeQuality
all individuals: 167
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variant carriers: 0

GenotypeQuality
all individuals: 1101
bin: 7.75e1
variant carriers: 2

East Asian
type: Population
allele count: 13
allele frequency: 2.845884413309983e-3
allele num: 4568
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 3018
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 31672
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 9.560229445506692e-5
allele num: 10460
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5336
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1364
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 390
num of homozygotes: 0

ClippingRankSum
type: SiteQuality
SIO_000300: -1.24e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: -1.33e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -1.133e0

FS
type: SiteQuality
SIO_000300: 7.84e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -9.2e-3

VQSLOD
type: SiteQuality
SIO_000300: -2.915e-1

DP
type: SiteQuality
SIO_000300: 9.33142e5

MQRankSum
type: SiteQuality
SIO_000300: -4.21e-1

MQ
type: SiteQuality
SIO_000300: 5.617e1

QD
type: SiteQuality
SIO_000300: 9.699999999999999e0

GenotypeQuality
all individuals: 336
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 380
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variant carriers: 0

GenotypeQuality
all individuals: 1024
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GenotypeQuality
all individuals: 1472
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
all individuals: 832
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
all individuals: 1070
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GenotypeQuality
all individuals: 12575
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variant carriers: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 392
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1396
num of homozygotes: 0

East Asian
type: Population
allele count: 1
allele frequency: 2.169197396963124e-4
allele num: 4610
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10520
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5374
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 3060
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 3.121293464011486e-5
allele num: 32038
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 2.911e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -8.800000000000001e-3

MQRankSum
type: SiteQuality
SIO_000300: -6.56e-1

DP
type: SiteQuality
SIO_000300: 9.35522e5

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.04e0

VQSLOD
type: SiteQuality
SIO_000300: -1.956e0

ClippingRankSum
type: SiteQuality
SIO_000300: 1.14e0

MQ
type: SiteQuality
SIO_000300: 5.766e1

BaseQRankSum
type: SiteQuality
SIO_000300: 1.43e0

QD
type: SiteQuality
SIO_000300: 6.83e0

GenotypeQuality
all individuals: 381
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2671
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
all individuals: 1433
bin: 2.75e1
variant carriers: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5486
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 400
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 3.024620410138528e-5
allele num: 33062
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 4746
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 3254
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10634
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1476
num of homozygotes: 0

QD
type: SiteQuality
SIO_000300: 1.727e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 4.27e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 1.64e0

VQSLOD
type: SiteQuality
SIO_000300: -8.731e-1

DP
type: SiteQuality
SIO_000300: 9.49606e5

FS
type: SiteQuality
SIO_000300: 1.536e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -8.1e-3

MQRankSum
type: SiteQuality
SIO_000300: 6.97e-1

MQ
type: SiteQuality
SIO_000300: 5.368e1

ClippingRankSum
type: SiteQuality
SIO_000300: -4.72e-1

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
all individuals: 1108
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variant carriers: 1

GenotypeQuality
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bin: 8.75e1
variant carriers: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1652
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 4982
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5700
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 3658
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 412
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10836
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 2.802533490275209e-5
allele num: 35682
num of homozygotes: 0

BaseQRankSum
type: SiteQuality
SIO_000300: -1.957e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -8.200000000000001e-3

ReadPosRankSum
type: SiteQuality
SIO_000300: -5.4e-1

MQ
type: SiteQuality
SIO_000300: 5.361e1

VQSLOD
type: SiteQuality
SIO_000300: -1.603e0

FS
type: SiteQuality
SIO_000300: 3.026e0

DP
type: SiteQuality
SIO_000300: 9.80218e5

QD
type: SiteQuality
SIO_000300: 7.08e0

MQRankSum
type: SiteQuality
SIO_000300: 3.36e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -8.51e-1

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
all individuals: 380
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GenotypeQuality
all individuals: 750
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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bin: 8.75e1
variant carriers: 0

South Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 10842
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5000
num of homozygotes: 0

Latino
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allele count: 0
allele frequency: 0.0e0
allele num: 3702
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1662
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5724
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 418
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 2
allele frequency: 5.580357142857143e-5
allele num: 35840
num of homozygotes: 0

InbreedingCoeff
type: SiteQuality
SIO_000300: -7.7e-3

DP
type: SiteQuality
SIO_000300: 9.80764e5

MQ
type: SiteQuality
SIO_000300: 5.425e1

FS
type: SiteQuality
SIO_000300: 1.333e0

MQRankSum
type: SiteQuality
SIO_000300: 1.35e-1

VQSLOD
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SIO_000300: -1.6e0

ReadPosRankSum
type: SiteQuality
SIO_000300: -4.24e-1

QD
type: SiteQuality
SIO_000300: 3.61e0

ClippingRankSum
type: SiteQuality
SIO_000300: 0.0e0

BaseQRankSum
type: SiteQuality
SIO_000300: -1.614e0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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bin: 5.75e1
variant carriers: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1772
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5788
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5134
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 3924
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 2.706359945872801e-5
allele num: 36950
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 434
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South Asian
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allele count: 0
allele frequency: 0.0e0
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MQRankSum
type: SiteQuality
SIO_000300: 1.27e0

FS
type: SiteQuality
SIO_000300: 1.2208e1

ReadPosRankSum
type: SiteQuality
SIO_000300: -1.164e0

ClippingRankSum
type: SiteQuality
SIO_000300: 7.41e-1

MQ
type: SiteQuality
SIO_000300: 5.705e1

VQSLOD
type: SiteQuality
SIO_000300: -2.811e0

BaseQRankSum
type: SiteQuality
SIO_000300: 6.35e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -7.1e-3

QD
type: SiteQuality
SIO_000300: 8.17e0

DP
type: SiteQuality
SIO_000300: 9.9004e5

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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bin: 7.25e1
variant carriers: 0

East Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 5146
num of homozygotes: 0

Latino
type: Population
allele count: 7
allele frequency: 1.773948302078054e-3
allele num: 3946
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 438
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5814
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1792
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 37174
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10990
num of homozygotes: 0

DP
type: SiteQuality
SIO_000300: 9.84756e5

FS
type: SiteQuality
SIO_000300: 0.0e0

MQRankSum
type: SiteQuality
SIO_000300: 7.1e-1

MQ
type: SiteQuality
SIO_000300: 5.485e1

BaseQRankSum
type: SiteQuality
SIO_000300: -1.173e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -7.5e-3

VQSLOD
type: SiteQuality
SIO_000300: -1.28e0

QD
type: SiteQuality
SIO_000300: 9.380000000000001e0

ReadPosRankSum
type: SiteQuality
SIO_000300: -3.61e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 2.01e-1

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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variant carriers: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5794
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 37040
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 9.112447603426281e-5
allele num: 10974
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5122
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 3940
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1784
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 436
num of homozygotes: 0

BaseQRankSum
type: SiteQuality
SIO_000300: 6.12e-1

DP
type: SiteQuality
SIO_000300: 9.67197e5

VQSLOD
type: SiteQuality
SIO_000300: -2.531e0

MQRankSum
type: SiteQuality
SIO_000300: 1.49e0

MQ
type: SiteQuality
SIO_000300: 5.951e1

QD
type: SiteQuality
SIO_000300: 4.39e0

FS
type: SiteQuality
SIO_000300: 1.76e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -8.500000000000001e-3

ClippingRankSum
type: SiteQuality
SIO_000300: -7.28e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: -4.37e-1

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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bin: 8.25e1
variant carriers: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 3844
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1742
num of homozygotes: 0

European (Non-Finnish)
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allele count: 2
allele frequency: 5.514199062586159e-5
allele num: 36270
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5734
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10912
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5022
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Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 426
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 4.123e0

QD
type: SiteQuality
SIO_000300: 9.470000000000001e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.07e-2

MQ
type: SiteQuality
SIO_000300: 6.0e1

BaseQRankSum
type: SiteQuality
SIO_000300: -4.29e-1

MQRankSum
type: SiteQuality
SIO_000300: -5.5e-1

VQSLOD
type: SiteQuality
SIO_000300: 1.25e0

ClippingRankSum
type: SiteQuality
SIO_000300: -2.18e-1

DP
type: SiteQuality
SIO_000300: 9.25956e5

ReadPosRankSum
type: SiteQuality
SIO_000300: 6.0e-3

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

African
type: Population
allele count: 12
allele frequency: 2.114910116320056e-3
allele num: 5674
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 406
num of homozygotes: 0

European (Non-Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 35590
num of homozygotes: 0

European (Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 1714
num of homozygotes: 0

South Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 10768
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 4880
num of homozygotes: 0

Latino
type: Population
allele count: 1
allele frequency: 2.676659528907923e-4
allele num: 3736
num of homozygotes: 0

ReadPosRankSum
type: SiteQuality
SIO_000300: -1.05e-1

VQSLOD
type: SiteQuality
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InbreedingCoeff
type: SiteQuality
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ClippingRankSum
type: SiteQuality
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BaseQRankSum
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DP
type: SiteQuality
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FS
type: SiteQuality
SIO_000300: 6.05e-1

MQRankSum
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SIO_000300: 1.43e-1

MQ
type: SiteQuality
SIO_000300: 5.748e1

QD
type: SiteQuality
SIO_000300: 1.228e1

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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bin: 8.25e1
variant carriers: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5644
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
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num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 4866
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 404
num of homozygotes: 0

South Asian
type: Population
allele count: 3
allele frequency: 2.791736460078169e-4
allele num: 10746
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 35482
num of homozygotes: 0

European (Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 1698
num of homozygotes: 0

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.4e-2

MQ
type: SiteQuality
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BaseQRankSum
type: SiteQuality
SIO_000300: -1.663e0

ReadPosRankSum
type: SiteQuality
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VQSLOD
type: SiteQuality
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MQRankSum
type: SiteQuality
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FS
type: SiteQuality
SIO_000300: 1.7375e1

QD
type: SiteQuality
SIO_000300: 1.094e1

DP
type: SiteQuality
SIO_000300: 8.78412e5

ClippingRankSum
type: SiteQuality
SIO_000300: -3.8e-1

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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bin: 6.25e1
variant carriers: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 3706
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1696
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 2.826136106714899e-5
allele num: 35384
num of homozygotes: 0

African
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allele count: 0
allele frequency: 0.0e0
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num of homozygotes: 0

East Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 4866
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
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num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
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num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 0.0e0

BaseQRankSum
type: SiteQuality
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InbreedingCoeff
type: SiteQuality
SIO_000300: 1.4e-2

DP
type: SiteQuality
SIO_000300: 8.77954e5

MQRankSum
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SIO_000300: 1.1e0

ClippingRankSum
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SIO_000300: 6.04e-1

ReadPosRankSum
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SIO_000300: -6.04e-1

MQ
type: SiteQuality
SIO_000300: 5.671e1

VQSLOD
type: SiteQuality
SIO_000300: -1.364e0

QD
type: SiteQuality
SIO_000300: 1.051e1

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
all individuals: 399
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 272
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 7362
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 925
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 86
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 380
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 736
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1077
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1040
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1112
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 75
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2036
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 2240
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 2102
bin: 3.25e1
variant carriers: 0

African
type: Population
allele count: 1
allele frequency: 1.77999288002848e-4
allele num: 5618
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 35184
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 396
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 4808
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 3610
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1694
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10682
num of homozygotes: 0

ReadPosRankSum
type: SiteQuality
SIO_000300: -1.122e0

DP
type: SiteQuality
SIO_000300: 8.66944e5

BaseQRankSum
type: SiteQuality
SIO_000300: 2.39e0

FS
type: SiteQuality
SIO_000300: 0.0e0

VQSLOD
type: SiteQuality
SIO_000300: -1.795e0

MQ
type: SiteQuality
SIO_000300: 5.615e1

QD
type: SiteQuality
SIO_000300: 8.35e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.6e-2

MQRankSum
type: SiteQuality
SIO_000300: -4.39e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 2.44e-1

GenotypeQuality
all individuals: 5745
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 22901
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 2863
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 302
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 109
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 253
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 184
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 164
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 79
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1478
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 16237
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 153
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 517
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 883
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 352
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 96
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1092
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 87
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 573
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 314
bin: 3.75e1
variant carriers: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 270
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 564
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2406
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 2.962085308056872e-4
allele num: 3376
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9002
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 120
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1272
num of homozygotes: 0

QD
type: SiteQuality
SIO_000300: 1.055e1

ReadPosRankSum
type: SiteQuality
SIO_000300: -7.81e-1

FS
type: SiteQuality
SIO_000300: 3.692e0

MQRankSum
type: SiteQuality
SIO_000300: 2.76e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -1.754e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.425e-1

DP
type: SiteQuality
SIO_000300: 8.00319e5

ClippingRankSum
type: SiteQuality
SIO_000300: 9.1e-1

VQSLOD
type: SiteQuality
SIO_000300: 3.09e0

MQ
type: SiteQuality
SIO_000300: 4.443e1

GenotypeQuality
all individuals: 91
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 67
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 321
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 15882
bin: 7.5e0
variant carriers: 1

GenotypeQuality
all individuals: 262
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 4064
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1824
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 548
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 23607
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 219
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 882
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 81
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 494
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 182
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 144
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 332
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 161
bin: 8.25e1
variant carriers: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 430
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1068
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7432
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 4.793863854266539e-4
allele num: 2086
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 214
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 3080
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 132
num of homozygotes: 0

ReadPosRankSum
type: SiteQuality
SIO_000300: -4.7e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 4.7e-1

MQRankSum
type: SiteQuality
SIO_000300: 3.36e-1

FS
type: SiteQuality
SIO_000300: 0.0e0

VQSLOD
type: SiteQuality
SIO_000300: -8.718e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.494e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -1.098e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

QD
type: SiteQuality
SIO_000300: 7.02e0

DP
type: SiteQuality
SIO_000300: 7.9401e5

GenotypeQuality
all individuals: 4015
bin: 2.25e1
variant carriers: 1

GenotypeQuality
all individuals: 14950
bin: 7.5e0
variant carriers: 2

GenotypeQuality
all individuals: 24547
bin: 2.5e0
variant carriers: 5

GenotypeQuality
all individuals: 303
bin: 9.75e1
variant carriers: 16

GenotypeQuality
all individuals: 105
bin: 5.25e1
variant carriers: 1

GenotypeQuality
all individuals: 164
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1920
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 61
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3112
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 166
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 747
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 212
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 300
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 126
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 75
bin: 9.25e1
variant carriers: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 102
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7830
num of homozygotes: 0

African
type: Population
allele count: 16
allele frequency: 7.889546351084813e-3
allele num: 2028
num of homozygotes: 2

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 318
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2024
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 384
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 856
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 3.386e0

MQRankSum
type: SiteQuality
SIO_000300: -6.34e-1

MQ
type: SiteQuality
SIO_000300: 5.52e1

VQSLOD
type: SiteQuality
SIO_000300: 7.37e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.519e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 7.33e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -4.56e-1

DP
type: SiteQuality
SIO_000300: 7.89506e5

BaseQRankSum
type: SiteQuality
SIO_000300: -2.78e-1

QD
type: SiteQuality
SIO_000300: 2.51e0

GenotypeQuality
all individuals: 582
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 6087
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 191
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1339
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 21658
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 5875
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 483
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 326
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 2356
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 1020
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 220
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 566
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 777
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 944
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 379
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 690
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 319
bin: 8.75e1
variant carriers: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 3486
num of homozygotes: 0