9-139904716-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904716
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904716
    reference: chr 9
allele count: 1
allele frequency: 1.685431133283894e-5
allele num: 59332
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.*254G>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: ENST00000437791
  gene symbol: ABCA2
  hgvsc: ENST00000437791.2:n.121G>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: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.*374G>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.6282G>A
  hgvsp: ENST00000341511.6:c.6282G>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.6279G>A
  hgvsp: ENST00000371605.3:c.6279G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.163-140G>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.6282G>A
  hgvsp: ENST00000265662.5:c.6282G>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: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.*3437G>A
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 499
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14434
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3734
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7512
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4576
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3857
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 25131
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 332
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3159
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 30380
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 26
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3096
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 14
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1415
  bin: 1.25e1
  variant carriers: 0
hgvs: p.Lys2094Lys
num of homozygotes: 0
population: African
population: Other
population: European (Non-Finnish)
population: East Asian
population: European (Finnish)
population: Latino
population: South Asian
reference allele: C
site quality: InbreedingCoeff
site quality: DP
site quality: MQRankSum
site quality: FS
site quality: ReadPosRankSum
site quality: ClippingRankSum
site quality: VQSLOD
site quality: QD
site quality: MQ
site quality: BaseQRankSum

9-139904722-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904722
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904722
    reference: chr 9
allele count: 1788
allele frequency: 3.147222417799057e-2
allele num: 56812
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000437791
  gene symbol: ABCA2
  hgvsc: ENST00000437791.2:n.115G>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.6273G>A
  hgvsp: ENST00000371605.3:c.6273G>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.6276G>A
  hgvsp: ENST00000265662.5:c.6276G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.163-146G>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: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.*368G>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: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.*3431G>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.6276G>A
  hgvsp: ENST00000341511.6:c.6276G>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: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.*248G>A
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 18
  bin: 6.75e1
  variant carriers: 18
genotype depth: GenotypeDepth
  all individuals: 14215
  bin: 1.25e1
  variant carriers: 669
genotype depth: GenotypeDepth
  all individuals: 6902
  bin: 2.25e1
  variant carriers: 199
genotype depth: GenotypeDepth
  all individuals: 26
  bin: 8.75e1
  variant carriers: 26
genotype depth: GenotypeDepth
  all individuals: 4892
  bin: 2.5e0
  variant carriers: 18
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 5.75e1
  variant carriers: 10
genotype depth: GenotypeDepth
  all individuals: 25
  bin: 4.25e1
  variant carriers: 13
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 4.75e1
  variant carriers: 5
genotype depth: GenotypeDepth
  all individuals: 3503
  bin: 2.75e1
  variant carriers: 60
genotype depth: GenotypeDepth
  all individuals: 20
  bin: 8.25e1
  variant carriers: 19
genotype depth: GenotypeDepth
  all individuals: 25675
  bin: 7.5e0
  variant carriers: 341
genotype depth: GenotypeDepth
  all individuals: 23
  bin: 9.25e1
  variant carriers: 23
genotype depth: GenotypeDepth
  all individuals: 3752
  bin: 1.75e1
  variant carriers: 498
genotype depth: GenotypeDepth
  all individuals: 23
  bin: 5.25e1
  variant carriers: 21
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 3.75e1
  variant carriers: 16
genotype depth: GenotypeDepth
  all individuals: 19
  bin: 6.25e1
  variant carriers: 18
genotype depth: GenotypeDepth
  all individuals: 20
  bin: 7.25e1
  variant carriers: 19
genotype depth: GenotypeDepth
  all individuals: 466
  bin: 3.25e1
  variant carriers: 23
genotype depth: GenotypeDepth
  all individuals: 114
  bin: 9.75e1
  variant carriers: 114
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 7.75e1
  variant carriers: 11
genotype quality: GenotypeQuality
  all individuals: 8760
  bin: 6.25e1
  variant carriers: 14
genotype quality: GenotypeQuality
  all individuals: 742
  bin: 6.75e1
  variant carriers: 27
genotype quality: GenotypeQuality
  all individuals: 173
  bin: 7.25e1
  variant carriers: 30
genotype quality: GenotypeQuality
  all individuals: 5087
  bin: 7.5e0
  variant carriers: 6
genotype quality: GenotypeQuality
  all individuals: 213
  bin: 5.75e1
  variant carriers: 24
genotype quality: GenotypeQuality
  all individuals: 442
  bin: 4.25e1
  variant carriers: 17
genotype quality: GenotypeQuality
  all individuals: 66
  bin: 8.75e1
  variant carriers: 54
hgvs: p.Ala2092Ala
num of homozygotes: 28
population: Latino
population: European (Finnish)
population: European (Non-Finnish)
population: Other
population: African
population: South Asian
population: East Asian
reference allele: C
site quality: ReadPosRankSum
site quality: FS
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: MQ
site quality: MQRankSum
site quality: ClippingRankSum
site quality: VQSLOD
site quality: QD
site quality: DP

9-139904727-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904727
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904727
    reference: chr 9
allele count: 1
allele frequency: 1.869438420698422e-5
allele num: 53492
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.163-151G>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: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.*243G>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.6268G>A
  hgvsp: ENSP00000360666.3:p.Gly2090Ser
  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: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.*363G>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.6271G>A
  hgvsp: ENSP00000265662.5:p.Gly2091Ser
  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: ENST00000437791
  gene symbol: ABCA2
  hgvsc: ENST00000437791.2:n.110G>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: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.*3426G>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.6271G>A
  hgvsp: ENSP00000344155.6:p.Gly2091Ser
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13633
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3546
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5388
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 27004
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3061
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 489
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6577
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1335
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 234
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 506
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2661
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 31
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 18
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1651
  bin: 1.25e1
  variant carriers: 0
hgvs: p.Gly2091Ser
num of homozygotes: 0
population: European (Non-Finnish)
population: Other
population: Latino
population: European (Finnish)
population: East Asian
population: African
population: South Asian
reference allele: C
site quality: BaseQRankSum
site quality: MQ
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: DP
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: ClippingRankSum
site quality: QD
site quality: FS

9-139904728-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904728
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904728
    reference: chr 9
allele count: 7
allele frequency: 1.318267419962335e-4
allele num: 53100
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.163-152C>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.6270C>T
  hgvsp: ENST00000341511.6:c.6270C>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: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.*242C>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: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.*3425C>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.6267C>T
  hgvsp: ENST00000371605.3:c.6267C>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.6270C>T
  hgvsp: ENST00000265662.5:c.6270C>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: ENST00000437791
  gene symbol: ABCA2
  hgvsc: ENST00000437791.2:n.109C>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: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.*362C>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3570
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 27123
  bin: 7.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2938
  bin: 1.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6636
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13566
  bin: 1.25e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5374
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 497
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 45
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 389
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2554
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 14
  bin: 8.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 603
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 128
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1632
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2703
  bin: 2.75e1
  variant carriers: 0
hgvs: p.Asn2090Asn
num of homozygotes: 0
population: African
population: Latino
population: European (Non-Finnish)
population: East Asian
population: South Asian
population: European (Finnish)
population: Other
reference allele: G
site quality: VQSLOD
site quality: ReadPosRankSum
site quality: DP
site quality: FS
site quality: MQ
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: ClippingRankSum
site quality: QD
site quality: BaseQRankSum

9-139904734-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904734
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904734
    reference: chr 9
allele count: 4
allele frequency: 7.941550190597205e-5
allele num: 50368
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.163-158C>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: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.*236C>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.6264C>T
  hgvsp: ENST00000265662.5:c.6264C>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: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.*356C>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: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.*3419C>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.6261C>T
  hgvsp: ENST00000371605.3:c.6261C>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: ENST00000437791
  gene symbol: ABCA2
  hgvsc: ENST00000437791.2:n.103C>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.6264C>T
  hgvsp: ENST00000341511.6:c.6264C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5990
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 487
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3439
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2700
  bin: 1.75e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 13125
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 27777
  bin: 7.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 44
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6155
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6198
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 588
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1729
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1180
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2408
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 303
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12
  bin: 8.75e1
  variant carriers: 0
hgvs: p.Gly2088Gly
num of homozygotes: 0
population: European (Non-Finnish)
population: South Asian
population: European (Finnish)
population: African
population: Other
population: East Asian
population: Latino
reference allele: G
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: DP
site quality: MQ
site quality: VQSLOD
site quality: MQRankSum
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: FS
site quality: QD

9-139904755-G-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904755
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904755
    reference: chr 9
allele count: 1
allele frequency: 2.247595073271599e-5
allele num: 44492
alternate allele: T
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.6243C>A
  hgvsp: ENST00000341511.6:c.6243C>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.6243C>A
  hgvsp: ENST00000265662.5:c.6243C>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: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.*3398C>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: ENST00000437791
  gene symbol: ABCA2
  hgvsc: ENST00000437791.2:n.82C>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: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.*215C>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.6240C>A
  hgvsp: ENST00000371605.3:c.6240C>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: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.*335C>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: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.163-179C>A
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1695
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3287
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7556
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5818
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29293
  bin: 7.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 11470
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 500
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7709
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 108
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 207
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 211
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 32
  bin: 8.25e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 17
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 622
  bin: 2.5e0
  variant carriers: 0
hgvs: p.Gly2081Gly
num of homozygotes: 0
population: European (Non-Finnish)
population: Other
population: African
population: South Asian
population: Latino
population: European (Finnish)
population: East Asian
reference allele: G
site quality: QD
site quality: ClippingRankSum
site quality: MQRankSum
site quality: VQSLOD
site quality: ReadPosRankSum
site quality: BaseQRankSum
site quality: DP
site quality: InbreedingCoeff
site quality: FS
site quality: MQ

9-139904762-C-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904762
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904762
    reference: chr 9
allele count: 1
allele frequency: 2.318141777551115e-5
allele num: 43138
alternate allele: G
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.6236G>C
  hgvsp: ENSP00000344155.6:p.Arg2079Pro
  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: ENST00000437791
  gene symbol: ABCA2
  hgvsc: ENST00000437791.2:n.75G>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: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.*208G>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: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.*3391G>C
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.163-186G>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.6236G>C
  hgvsp: ENSP00000265662.5:p.Arg2079Pro
  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.6233G>C
  hgvsp: ENSP00000360666.3:p.Arg2078Pro
  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: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.*328G>C
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8209
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1413
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 494
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29541
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11054
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3257
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5610
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 44
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 762
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 30
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1961
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 18
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1373
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 186
  bin: 4.25e1
  variant carriers: 0
hgvs: p.Arg2079Pro
num of homozygotes: 0
population: South Asian
population: European (Non-Finnish)
population: Other
population: Latino
population: African
population: East Asian
population: European (Finnish)
reference allele: C
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: FS
site quality: MQRankSum
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: QD
site quality: MQ
site quality: ClippingRankSum
site quality: DP

9-139904762-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904762
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904762
    reference: chr 9
allele count: 1
allele frequency: 2.318141777551115e-5
allele num: 43138
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.6236G>A
  hgvsp: ENSP00000344155.6:p.Arg2079His
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.163-186G>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.6233G>A
  hgvsp: ENSP00000360666.3:p.Arg2078His
  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: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.*208G>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.6236G>A
  hgvsp: ENSP00000265662.5:p.Arg2079His
  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: ENST00000437791
  gene symbol: ABCA2
  hgvsc: ENST00000437791.2:n.75G>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: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.*3391G>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: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.*328G>A
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 29541
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1413
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8209
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 494
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5610
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11054
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 44
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3257
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8048
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1373
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 684
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8387
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1961
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 191
  bin: 4.75e1
  variant carriers: 0
hgvs: p.Arg2079His
num of homozygotes: 0
population: European (Finnish)
population: South Asian
population: Latino
population: European (Non-Finnish)
population: African
population: Other
population: East Asian
reference allele: C
site quality: MQ
site quality: MQRankSum
site quality: ClippingRankSum
site quality: ReadPosRankSum
site quality: FS
site quality: DP
site quality: QD
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: VQSLOD

9-139904781-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904781
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904781
    reference: chr 9
allele count: 1
allele frequency: 2.740627055470292e-5
allele num: 36488
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.6217C>T
  hgvsp: ENSP00000265662.5:p.Arg2073Cys
  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: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.*189C>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.6214C>T
  hgvsp: ENSP00000360666.3:p.Arg2072Cys
  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: ENST00000437791
  gene symbol: ABCA2
  hgvsc: ENST00000437791.2:n.56C>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: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.163-205C>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.6217C>T
  hgvsp: ENSP00000344155.6:p.Arg2073Cys
  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: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.*3372C>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: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.*309C>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 946
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3162
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 484
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11412
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29157
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9287
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4822
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 42
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 414
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 149
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1390
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 103
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 770
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 702
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 31667
  bin: 2.25e1
  variant carriers: 0
hgvs: p.Arg2073Cys
num of homozygotes: 0
population: Latino
population: European (Finnish)
population: East Asian
population: African
population: South Asian
population: European (Non-Finnish)
population: Other
reference allele: G
site quality: MQRankSum
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: QD
site quality: DP
site quality: InbreedingCoeff
site quality: FS
site quality: ClippingRankSum
site quality: MQ
site quality: VQSLOD

9-139904787-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904787
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904787
    reference: chr 9
allele count: 1
allele frequency: 2.887336143673847e-5
allele num: 34634
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.6211G>A
  hgvsp: ENSP00000265662.5:p.Val2071Ile
  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: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.*183G>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.6208G>A
  hgvsp: ENSP00000360666.3:p.Val2070Ile
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.163-211G>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.6211G>A
  hgvsp: ENSP00000344155.6:p.Val2071Ile
  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: ENST00000437791
  gene symbol: ABCA2
  hgvsc: ENST00000437791.2:n.50G>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: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.*3366G>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: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.*303G>A
  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: 4562
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 28613
  bin: 7.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 483
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 822
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 42
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3127
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12825
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8698
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 118
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 377
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1238
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2527
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 935
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 23
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 12908
  bin: 7.5e0
  variant carriers: 0
hgvs: p.Val2071Ile
num of homozygotes: 0
population: East Asian
population: Other
population: South Asian
population: European (Finnish)
population: African
population: European (Non-Finnish)
population: Latino
reference allele: C
site quality: VQSLOD
site quality: FS
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: MQ
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: QD
site quality: MQRankSum
site quality: DP

9-139904788-G-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904788
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904788
    reference: chr 9
allele count: 1
allele frequency: 2.920560747663552e-5
allele num: 34240
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.6210C>A
  hgvsp: ENST00000265662.5:c.6210C>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: ENST00000437791
  gene symbol: ABCA2
  hgvsc: ENST00000437791.2:n.49C>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.6210C>A
  hgvsp: ENST00000341511.6:c.6210C>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.163-212C>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: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.*3365C>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.6207C>A
  hgvsp: ENST00000371605.3:c.6207C>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: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.*182C>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: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.*302C>A
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: VQSRTrancheSNP99.60to99.80
genotype depth: GenotypeDepth
  all individuals: 8609
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 28522
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4522
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 40
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 782
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13076
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3116
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 482
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 361
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 898
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 30519
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 143
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2532
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 693
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1410
  bin: 1.25e1
  variant carriers: 0
hgvs: p.Ala2070Ala
num of homozygotes: 0
population: Latino
population: South Asian
population: European (Non-Finnish)
population: Other
population: East Asian
population: African
population: European (Finnish)
reference allele: G
site quality: ClippingRankSum
site quality: FS
site quality: MQRankSum
site quality: DP
site quality: VQSLOD
site quality: MQ
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: QD

9-139904793-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904793
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904793
    reference: chr 9
allele count: 1
allele frequency: 3.067861087249969e-5
allele num: 32596
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.6202C>T
  hgvsp: ENST00000371605.3:c.6202C>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: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.*177C>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: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.*297C>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: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.163-217C>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: ENST00000437791
  gene symbol: ABCA2
  hgvsc: ENST00000437791.2:n.44C>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.6205C>T
  hgvsp: ENST00000341511.6:c.6205C>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.6205C>T
  hgvsp: ENST00000265662.5:c.6205C>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: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.*3360C>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 3082
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8021
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 673
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 27936
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4330
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 473
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 39
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14477
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6784
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 96
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 60
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 665
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 14545
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 89
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 678
  bin: 6.75e1
  variant carriers: 0
hgvs: p.Leu2069Leu
num of homozygotes: 0
population: European (Finnish)
population: South Asian
population: Latino
population: African
population: East Asian
population: European (Non-Finnish)
population: Other
reference allele: G
site quality: MQRankSum
site quality: FS
site quality: ClippingRankSum
site quality: QD
site quality: DP
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: MQ
site quality: InbreedingCoeff

9-139904796-T-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904796
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904796
    reference: chr 9
allele count: 1
allele frequency: 3.137156481365291e-5
allele num: 31876
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.*294A>G
  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.6199A>G
  hgvsp: ENSP00000360666.3:p.Ile2067Val
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.163-220A>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.6202A>G
  hgvsp: ENSP00000344155.6:p.Ile2068Val
  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: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.*174A>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: ENST00000437791
  gene symbol: ABCA2
  hgvsc: ENST00000437791.2:n.41A>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.6202A>G
  hgvsp: ENSP00000265662.5:p.Ile2068Val
  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: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.*3357A>G
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: VQSRTrancheSNP99.60to99.80
genotype depth: GenotypeDepth
  all individuals: 7755
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 478
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4227
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 39
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 603
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15333
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3052
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 27472
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 286
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 140
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 54
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 86
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2501
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 29040
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 762
  bin: 3.25e1
  variant carriers: 0
hgvs: p.Ile2068Val
num of homozygotes: 0
population: European (Non-Finnish)
population: European (Finnish)
population: African
population: East Asian
population: Latino
population: South Asian
population: Other
reference allele: T
site quality: MQRankSum
site quality: VQSLOD
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: DP
site quality: MQ
site quality: ClippingRankSum
site quality: FS
site quality: ReadPosRankSum
site quality: QD

9-139904798-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904798
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904798
    reference: chr 9
allele count: 1
allele frequency: 3.224974200206398e-5
allele num: 31008
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000437791
  gene symbol: ABCA2
  hgvsc: ENST00000437791.2:n.39G>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.6200G>A
  hgvsp: ENSP00000265662.5:p.Arg2067His
  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: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.*172G>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.6200G>A
  hgvsp: ENSP00000344155.6:p.Arg2067His
  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: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.*292G>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: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.163-222G>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.6197G>A
  hgvsp: ENSP00000360666.3:p.Arg2066His
  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: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.*3355G>A
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 631
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 27052
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7612
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 4156
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 40
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15904
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3036
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 477
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  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: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 670
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 79
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2467
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 15983
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 22
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 14
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1405
  bin: 1.25e1
  variant carriers: 0
hgvs: p.Arg2067His
num of homozygotes: 0
population: European (Finnish)
population: South Asian
population: East Asian
population: African
population: Latino
population: Other
population: European (Non-Finnish)
reference allele: C
site quality: MQRankSum
site quality: BaseQRankSum
site quality: FS
site quality: VQSLOD
site quality: ClippingRankSum
site quality: MQ
site quality: ReadPosRankSum
site quality: InbreedingCoeff
site quality: DP
site quality: QD

9-139904799-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904799
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904799
    reference: chr 9
allele count: 0
allele frequency: 0.0e0
allele num: 30744
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.*3354C>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.6199C>T
  hgvsp: ENSP00000344155.6:p.Arg2067Cys
  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.6196C>T
  hgvsp: ENSP00000360666.3:p.Arg2066Cys
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.163-223C>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: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.*171C>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: ENST00000437791
  gene symbol: ABCA2
  hgvsc: ENST00000437791.2:n.38C>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.6199C>T
  hgvsp: ENSP00000265662.5:p.Arg2067Cys
  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: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.*291C>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: AC_Adj0_Filter
genotype depth: GenotypeDepth
  all individuals: 12
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 26933
  bin: 7.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16247
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4116
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3033
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7486
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 559
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 472
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 39
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 28351
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2374
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 676
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 984
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 75
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 90
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 16310
  bin: 7.5e0
  variant carriers: 0
hgvs: p.Arg2067Cys
num of homozygotes: 0
population: South Asian
population: European (Non-Finnish)
population: Other
population: Latino
population: East Asian
population: European (Finnish)
population: African
reference allele: G
site quality: MQRankSum
site quality: VQSLOD
site quality: QD
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: FS
site quality: MQ
site quality: BaseQRankSum
site quality: DP
site quality: ReadPosRankSum

9-139904810-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904810
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904810
    reference: chr 9
allele count: 2
allele frequency: 7.373000073730001e-5
allele num: 27126
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.*3343G>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.6188G>A
  hgvsp: ENSP00000344155.6:p.Arg2063Gln
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.163-234G>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.6185G>A
  hgvsp: ENSP00000360666.3:p.Arg2062Gln
  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: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.*160G>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: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.*280G>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: ENST00000437791
  gene symbol: ABCA2
  hgvsc: ENST00000437791.2:n.27G>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.6188G>A
  hgvsp: ENSP00000265662.5:p.Arg2063Gln
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 425
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 24293
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3692
  bin: 2.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 15
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 454
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 37
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2924
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6357
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20229
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 22
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1561
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 170
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 140
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 63
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 514
  bin: 3.25e1
  variant carriers: 0
hgvs: p.Arg2063Gln
num of homozygotes: 0
population: European (Non-Finnish)
population: Other
population: European (Finnish)
population: African
population: Latino
population: South Asian
population: East Asian
reference allele: C
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: FS
site quality: QD
site quality: MQRankSum
site quality: DP
site quality: ReadPosRankSum
site quality: BaseQRankSum
site quality: MQ
site quality: ClippingRankSum

9-139904811-G-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904811
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904811
    reference: chr 9
allele count: 1
allele frequency: 3.798237617745366e-5
allele num: 26328
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.*159C>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.6184C>A
  hgvsp: ENST00000371605.3:c.6184C>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: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.*279C>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.6187C>A
  hgvsp: ENST00000265662.5:c.6187C>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.163-235C>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.6187C>A
  hgvsp: ENST00000341511.6:c.6187C>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: ENST00000437791
  gene symbol: ABCA2
  hgvsc: ENST00000437791.2:n.26C>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: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.*3342C>A
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 23691
  bin: 7.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 21068
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 440
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6106
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 411
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3624
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2893
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 39
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 22
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1024
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 84
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 60
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 66
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 768
  bin: 2.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 10
  bin: 8.75e1
  variant carriers: 0
hgvs: p.Arg2063Arg
num of homozygotes: 0
population: South Asian
population: Latino
population: African
population: European (Finnish)
population: European (Non-Finnish)
population: East Asian
population: Other
reference allele: G
site quality: QD
site quality: MQ
site quality: MQRankSum
site quality: FS
site quality: ClippingRankSum
site quality: ReadPosRankSum
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: BaseQRankSum
site quality: DP

9-139904834-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904834
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904834
    reference: chr 9
allele count: 0
allele frequency: 0.0e0
allele num: 20588
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.6175-11C>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.6175-11C>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: ENST00000437791
  gene symbol: ABCA2
  hgvsc: ENST00000437791.2:n.3C>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.6172-11C>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: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.*136C>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: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+238C>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.*3330-11C>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.*267-11C>T
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: 3' UTR
filter: AC_Adj0_Filter
genotype depth: GenotypeDepth
  all individuals: 17346
  bin: 7.5e0
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 394
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2795
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2519
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4296
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 398
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 36
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 28753
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1751
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 38
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 118
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 137
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 376
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 47
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4879
  bin: 6.25e1
  variant carriers: 0
num of homozygotes: 0
population: Other
population: East Asian
population: European (Finnish)
population: South Asian
population: African
population: Latino
population: European (Non-Finnish)
reference allele: G
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: MQRankSum
site quality: FS
site quality: VQSLOD
site quality: MQ
site quality: ReadPosRankSum
site quality: ClippingRankSum
site quality: DP
site quality: QD

http://identifiers.org/exac.variant/9-139904835-C-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904835
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904835
    reference: chr 9
allele count: 1
allele frequency: 4.950985246063966e-5
allele num: 20198
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+237G>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.6172-12G>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.6175-12G>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.6175-12G>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.*267-12G>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: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.*135G>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: ENST00000437791
  gene symbol: ABCA2
  hgvsc: ENST00000437791.2:n.2G>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.*3330-12G>T
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: 3' UTR
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29238
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2462
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 395
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16827
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4283
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 37
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 443
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2635
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1856
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 49
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 410
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 18
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 54
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1427
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4624
  bin: 6.25e1
  variant carriers: 0
num of homozygotes: 0
population: Other
population: East Asian
population: European (Finnish)
population: South Asian
population: European (Non-Finnish)
population: Latino
population: African
reference allele: C
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: BaseQRankSum
site quality: QD
site quality: ReadPosRankSum
site quality: DP
site quality: ClippingRankSum
site quality: FS
site quality: MQ

9-139904838-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904838
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904838
    reference: chr 9
allele count: 0
allele frequency: 0.0e0
allele num: 19326
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.*132C>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: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+234C>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.*3330-15C>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.*267-15C>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.6172-15C>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.6175-15C>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.6175-15C>T
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: 3' UTR
filter: AC_Adj0_Filter
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4351
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15430
  bin: 7.5e0
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2182
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2303
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 364
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 606
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 37
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 30304
  bin: 2.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 30153
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2046
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 58
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 483
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13270
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 203
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 22
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 4040
  bin: 6.25e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 108
  bin: 5.75e1
  variant carriers: 1
num of homozygotes: 0
population: Latino
population: East Asian
population: South Asian
population: European (Non-Finnish)
population: African
population: European (Finnish)
population: Other
reference allele: G
site quality: MQ
site quality: InbreedingCoeff
site quality: FS
site quality: DP
site quality: MQRankSum
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: VQSLOD
site quality: QD
site quality: ReadPosRankSum

9-139904842-A-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904842
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904842
    reference: chr 9
allele count: 0
allele frequency: 0.0e0
allele num: 18518
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.6172-19T>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.*267-19T>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: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.*128T>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.6175-19T>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.6175-19T>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: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+230T>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.*3330-19T>A
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: 3' UTR
filter: AC_Adj0_Filter
genotype depth: GenotypeDepth
  all individuals: 744
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 31067
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 326
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14477
  bin: 7.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 34
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2065
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1956
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4322
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 52
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1796
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 50
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2190
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2108
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12174
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 30804
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 66
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 696
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 243
  bin: 3.75e1
  variant carriers: 0
num of homozygotes: 0
population: Latino
population: South Asian
population: European (Finnish)
population: Other
population: East Asian
population: European (Non-Finnish)
population: African
reference allele: A
site quality: MQ
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: FS
site quality: DP
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: QD
site quality: MQRankSum

9-139904848-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904848
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904848
    reference: chr 9
allele count: 1
allele frequency: 5.803156917363046e-5
allele num: 17232
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.6172-25G>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.*3330-25G>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: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+224G>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: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.*122G>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.*267-25G>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.6175-25G>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.6175-25G>A
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: 3' UTR
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 290
  bin: 3.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1727
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4194
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1539
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 31734
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13183
  bin: 7.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 29
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1032
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 698
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 75
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2890
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1635
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 65
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 70
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 22
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 2581
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2360
  bin: 1.25e1
  variant carriers: 0
num of homozygotes: 0
population: Latino
population: Other
population: South Asian
population: European (Finnish)
population: East Asian
population: African
population: European (Non-Finnish)
reference allele: C
site quality: MQ
site quality: VQSLOD
site quality: MQRankSum
site quality: QD
site quality: FS
site quality: ClippingRankSum
site quality: ReadPosRankSum
site quality: InbreedingCoeff
site quality: DP
site quality: BaseQRankSum

9-139904849-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904849
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904849
    reference: chr 9
allele count: 0
allele frequency: 0.0e0
allele num: 16712
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.6175-26C>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: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+223C>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.6175-26C>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.*3330-26C>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.*267-26C>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.6172-26C>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: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.*121C>T
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: 3' UTR
filter: AC_Adj0_Filter
genotype depth: GenotypeDepth
  all individuals: 31
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 31852
  bin: 2.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1591
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 252
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1384
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1187
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12731
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  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: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4100
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2550
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 64
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 31164
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2850
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 61
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 38
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 80
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 115
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 8.75e1
  variant carriers: 0
num of homozygotes: 0
population: Other
population: European (Finnish)
population: Latino
population: European (Non-Finnish)
population: East Asian
population: African
population: South Asian
reference allele: G
site quality: BaseQRankSum
site quality: MQRankSum
site quality: VQSLOD
site quality: FS
site quality: ReadPosRankSum
site quality: ClippingRankSum
site quality: QD
site quality: MQ
site quality: InbreedingCoeff
site quality: DP

9-139904850-G-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904850
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904850
    reference: chr 9
allele count: 1
allele frequency: 5.967299200381907e-5
allele num: 16758
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.*120C>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.6172-27C>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.6175-27C>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.*267-27C>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.6175-27C>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: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+222C>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.*3330-27C>G
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: 3' UTR
filter: VQSRTrancheSNP99.60to99.80
genotype depth: GenotypeDepth
  all individuals: 1173
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12688
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 27
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 31932
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1393
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1592
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4095
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 243
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2635
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 778
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 64
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 75
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 292
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 847
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 75
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2590
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 64
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 8.75e1
  variant carriers: 0
num of homozygotes: 0
population: African
population: Latino
population: East Asian
population: Other
population: European (Finnish)
population: South Asian
population: European (Non-Finnish)
reference allele: G
site quality: QD
site quality: VQSLOD
site quality: ReadPosRankSum
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: MQ
site quality: FS
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: DP

9-139904866-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904866
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904866
    reference: chr 9
allele count: 1
allele frequency: 7.457121551081282e-5
allele num: 13410
alternate allele: T
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.*3330-43G>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.6172-43G>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: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.*104G>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.6175-43G>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: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+206G>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.*267-43G>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.6175-43G>A
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: 3' UTR
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 492
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1021
  bin: 2.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2060
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3182
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 30970
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 19
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 144
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11453
  bin: 7.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 25
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1012
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 239
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1128
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 775
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4909
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 36
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 36
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 30
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 27398
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3917
  bin: 1.25e1
  variant carriers: 0
num of homozygotes: 0
population: Latino
population: African
population: East Asian
population: European (Finnish)
population: European (Non-Finnish)
population: Other
population: South Asian
reference allele: C
site quality: ReadPosRankSum
site quality: FS
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: MQ
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: VQSLOD
site quality: DP
site quality: QD

9-139904870-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904870
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904870
    reference: chr 9
allele count: 2
allele frequency: 1.754693805930865e-4
allele num: 11398
alternate allele: A
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.*267-47C>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.6175-47C>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: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+202C>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.6175-47C>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: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.*100C>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.6172-47C>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.*3330-47C>T
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: 3' UTR
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1902
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2949
  bin: 1.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 117
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 30
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 396
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11340
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 19
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 30714
  bin: 2.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1062
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 287
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 14
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 15
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4008
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1091
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3157
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 22628
  bin: 7.5e0
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 3531
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 106
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 733
  bin: 3.75e1
  variant carriers: 0
num of homozygotes: 0
population: European (Non-Finnish)
population: East Asian
population: African
population: Other
population: South Asian
population: Latino
population: European (Finnish)
reference allele: G
site quality: FS
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: ClippingRankSum
site quality: ReadPosRankSum
site quality: MQ
site quality: MQRankSum
site quality: DP
site quality: BaseQRankSum
site quality: QD

9-139904923-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904923
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904923
    reference: chr 9
allele count: 0
allele frequency: 0.0e0
allele num: 9614
alternate allele: A
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.6175-100C>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.*3330-100C>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: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+149C>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.6172-100C>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.6175-100C>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.*267-100C>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: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.*47C>T
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: 3' UTR
filter: AC_Adj0_Filter
genotype depth: GenotypeDepth
  all individuals: 18723
  bin: 7.5e0
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 729
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3993
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 41
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 28978
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 186
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 23
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 30
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 35
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 40
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 97
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 29
  bin: 7.25e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 24
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 135
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6884
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7603
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 19985
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6533
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 73
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 514
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1342
  bin: 3.25e1
  variant carriers: 0
num of homozygotes: 0
population: African
population: Latino
population: European (Finnish)
population: East Asian
population: Other
population: European (Non-Finnish)
population: South Asian
reference allele: G
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: DP
site quality: MQ
site quality: FS
site quality: VQSLOD
site quality: MQRankSum
site quality: QD

9-139904928-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904928
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904928
    reference: chr 9
allele count: 41
allele frequency: 4.280643140530382e-3
allele num: 9578
alternate allele: A
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.*3330-105C>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: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+144C>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.6172-105C>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.*267-105C>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.6175-105C>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: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.*42C>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.6175-105C>T
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: 3' UTR
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 18961
  bin: 7.5e0
  variant carriers: 45
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 36
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 30
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 23
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 39
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4018
  bin: 1.25e1
  variant carriers: 29
genotype depth: GenotypeDepth
  all individuals: 700
  bin: 1.75e1
  variant carriers: 12
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 28676
  bin: 2.5e0
  variant carriers: 8
genotype depth: GenotypeDepth
  all individuals: 230
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 97
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1584
  bin: 2.75e1
  variant carriers: 4
genotype quality: GenotypeQuality
  all individuals: 24
  bin: 8.25e1
  variant carriers: 4
genotype quality: GenotypeQuality
  all individuals: 519
  bin: 3.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 6290
  bin: 1.25e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 5652
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12
  bin: 5.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 130
  bin: 4.25e1
  variant carriers: 3
genotype quality: GenotypeQuality
  all individuals: 52
  bin: 5.25e1
  variant carriers: 5
genotype quality: GenotypeQuality
  all individuals: 32
  bin: 7.75e1
  variant carriers: 8
genotype quality: GenotypeQuality
  all individuals: 124
  bin: 4.75e1
  variant carriers: 2
num of homozygotes: 0
population: European (Non-Finnish)
population: European (Finnish)
population: East Asian
population: African
population: Other
population: Latino
population: South Asian
reference allele: G
site quality: FS
site quality: DP
site quality: InbreedingCoeff
site quality: MQ
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: VQSLOD
site quality: QD

9-139904937-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904937
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904937
    reference: chr 9
allele count: 1
allele frequency: 9.607993850883935e-5
allele num: 10408
alternate allele: G
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.*267-114T>C
  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.*3330-114T>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: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.*33T>C
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+135T>C
  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.6175-114T>C
  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.6172-114T>C
  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.6175-114T>C
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: 3' UTR
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 23
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 410
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 55
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20905
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 135
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 30
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 26825
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4473
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 40
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 710
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 36
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 104
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 138
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 389
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4827
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 24
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4409
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1332
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 28
  bin: 5.25e1
  variant carriers: 0
num of homozygotes: 0
population: African
population: South Asian
population: East Asian
population: European (Non-Finnish)
population: Latino
population: European (Finnish)
population: Other
reference allele: A
site quality: QD
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: MQ
site quality: ReadPosRankSum
site quality: FS
site quality: BaseQRankSum
site quality: VQSLOD
site quality: DP
site quality: ClippingRankSum

http://identifiers.org/exac.variant/9-139904939-C-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904939
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904939
    reference: chr 9
allele count: 0
allele frequency: 0.0e0
allele num: 10794
alternate allele: A
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.*3330-116G>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.6175-116G>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.6175-116G>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.*267-116G>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: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.*31G>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.6172-116G>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: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+133G>T
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: 3' UTR
filter: AC_Adj0_Filter
genotype depth: GenotypeDepth
  all individuals: 55
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 37
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 42
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 30
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 778
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 138
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 424
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4811
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 21454
  bin: 7.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 26000
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 23
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 139
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 117
  bin: 9.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1763
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 25
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 78
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 316
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1385
  bin: 3.25e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 14278
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3763
  bin: 1.75e1
  variant carriers: 0
num of homozygotes: 0
population: African
population: European (Finnish)
population: South Asian
population: East Asian
population: Latino
population: Other
population: European (Non-Finnish)
reference allele: C
site quality: FS
site quality: VQSLOD
site quality: MQ
site quality: MQRankSum
site quality: ClippingRankSum
site quality: DP
site quality: QD
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: ReadPosRankSum

http://identifiers.org/exac.variant/9-139904940-C-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904940
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904940
    reference: chr 9
allele count: 0
allele frequency: 0.0e0
allele num: 11790
alternate allele: A
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.6175-117G>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.*267-117G>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: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+132G>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.6175-117G>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: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.*30G>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.6172-117G>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.*3330-117G>T
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: 3' UTR
filter: AC_Adj0
genotype depth: GenotypeDepth
  all individuals: 61
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 25485
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 41
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 156
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 31
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 813
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 23
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 37
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4957
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 21959
  bin: 7.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 454
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 9.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 15877
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3329
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 27
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 88
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 135
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1498
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21613
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 556
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 38
  bin: 7.25e1
  variant carriers: 0
num of homozygotes: 0
population: East Asian
population: African
population: Latino
population: South Asian
population: European (Finnish)
population: Other
population: European (Non-Finnish)
reference allele: C
site quality: MQRankSum
site quality: QD
site quality: InbreedingCoeff
site quality: MQ
site quality: VQSLOD
site quality: FS
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: ClippingRankSum
site quality: DP

9-139904940-C-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904940
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904940
    reference: chr 9
allele count: 1
allele frequency: 8.481764206955047e-5
allele num: 11790
alternate allele: G
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.6175-117G>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: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.*30G>C
  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.*267-117G>C
  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.*3330-117G>C
  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.6172-117G>C
  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.6175-117G>C
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+132G>C
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: 3' UTR
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 21959
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4957
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 41
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 156
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 37
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 25485
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 454
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 813
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 31
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 23
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 61
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 27
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 144
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 88
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 23
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21613
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 135
  bin: 4.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 38
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4349
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 556
  bin: 3.75e1
  variant carriers: 0
num of homozygotes: 0
population: East Asian
population: European (Finnish)
population: Other
population: South Asian
population: African
population: European (Non-Finnish)
population: Latino
reference allele: C
site quality: MQ
site quality: FS
site quality: ReadPosRankSum
site quality: DP
site quality: VQSLOD
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: QD

9-139904943-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904943
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904943
    reference: chr 9
allele count: 0
allele frequency: 0.0e0
allele num: 11744
alternate allele: G
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.6175-120T>C
  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.*267-120T>C
  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.*3330-120T>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: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.*27T>C
  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.6172-120T>C
  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.6175-120T>C
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+129T>C
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: 3' UTR
filter: AC_Adj0_Filter
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5787
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 23197
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 69
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 207
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 23693
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 978
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 615
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 31
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 38
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 23
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 546
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
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  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
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  bin: 2.75e1
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genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
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  variant carriers: 0
genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
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  bin: 1.75e1
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genotype quality: GenotypeQuality
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  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 19
  bin: 8.25e1
  variant carriers: 0
num of homozygotes: 0
population: East Asian
population: European (Finnish)
population: Latino
population: South Asian
population: African
population: European (Non-Finnish)
population: Other
reference allele: A
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: FS
site quality: VQSLOD
site quality: MQ
site quality: BaseQRankSum
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: QD
site quality: DP

9-139904958-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904958
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904958
    reference: chr 9
allele count: 2
allele frequency: 7.206168480219068e-5
allele num: 27754
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+114G>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.6174+114G>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.*266+114G>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.6171+114G>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.*3329+114G>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.6174+114G>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: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.*12G>A
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: 3' UTR
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11588
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 23
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
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  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 182
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 889
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1976
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  variant carriers: 1
genotype depth: GenotypeDepth
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  variant carriers: 0
genotype depth: GenotypeDepth
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  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
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  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
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  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
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  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 30588
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
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  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
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  bin: 2.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
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  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
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  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 60
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 9.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1478
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 450
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
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  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
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  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1112
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 252
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1427
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 382
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3071
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1977
  bin: 1.75e1
  variant carriers: 0
num of homozygotes: 0
population: European (Non-Finnish)
population: African
population: East Asian
population: European (Finnish)
population: South Asian
population: Latino
population: Other
reference allele: C
site quality: MQRankSum
site quality: BaseQRankSum
site quality: DP
site quality: FS
site quality: ClippingRankSum
site quality: ReadPosRankSum
site quality: QD
site quality: MQ
site quality: VQSLOD
site quality: InbreedingCoeff

9-139904959-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904959
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904959
    reference: chr 9
allele count: 1
allele frequency: 3.736083090487933e-5
allele num: 26766
alternate allele: G
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.*266+113T>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: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.*11T>C
  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.*3329+113T>C
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+113T>C
  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.6174+113T>C
  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.6174+113T>C
  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.6171+113T>C
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: 3' UTR
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 29720
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10548
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 67
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2365
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3815
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1072
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 23
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 222
  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: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9417
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3023
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 104
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2378
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2269
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 18
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1950
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3202
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 183
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1053
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2825
  bin: 2.75e1
  variant carriers: 0
num of homozygotes: 0
population: European (Non-Finnish)
population: Other
population: South Asian
population: European (Finnish)
population: African
population: Latino
population: East Asian
reference allele: A
site quality: QD
site quality: FS
site quality: VQSLOD
site quality: DP
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: MQ
site quality: ClippingRankSum

9-139904959-A-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904959
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904959
    reference: chr 9
allele count: 2
allele frequency: 7.472166180975865e-5
allele num: 26766
alternate allele: T
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.6174+113T>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: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+113T>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.*266+113T>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.6171+113T>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: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.*11T>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.*3329+113T>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.6174+113T>A
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: 3' UTR
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 29720
  bin: 7.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 23
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 222
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2365
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1072
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3815
  bin: 2.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 10548
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9417
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 67
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2269
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1053
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2825
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 313
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 19
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1950
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10854
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2378
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 99
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 27602
  bin: 2.25e1
  variant carriers: 0
num of homozygotes: 0
population: European (Non-Finnish)
population: Latino
population: East Asian
population: African
population: European (Finnish)
population: South Asian
population: Other
reference allele: A
site quality: QD
site quality: FS
site quality: VQSLOD
site quality: MQ
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: DP
site quality: BaseQRankSum
site quality: ClippingRankSum

9-139904961-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904961
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904961
    reference: chr 9
allele count: 1
allele frequency: 2.9049500348594e-5
allele num: 34424
alternate allele: T
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.6174+111G>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.6171+111G>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.6174+111G>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.*266+111G>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: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.*9G>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.*3329+111G>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: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+111G>A
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: 3' UTR
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 29681
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1328
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4743
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9510
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 281
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9351
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 23
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2449
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 48
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 75
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 428
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9336
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1414
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 60
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 22
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 185
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 172
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 29326
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 736
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3000
  bin: 3.25e1
  variant carriers: 0
num of homozygotes: 0
population: East Asian
population: Other
population: African
population: European (Finnish)
population: Latino
population: European (Non-Finnish)
population: South Asian
reference allele: C
site quality: MQRankSum
site quality: VQSLOD
site quality: ReadPosRankSum
site quality: DP
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: FS
site quality: MQ
site quality: ClippingRankSum
site quality: QD

9-139904963-C-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904963
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904963
    reference: chr 9
allele count: 2
allele frequency: 5.279273571956499e-5
allele num: 37884
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.6171+109G>C
  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.6174+109G>C
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+109G>C
  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.*3329+109G>C
  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.6174+109G>C
  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.*266+109G>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: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.*7G>C
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: 3' UTR
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 8107
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6151
  bin: 2.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 53
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29526
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 23
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1538
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9335
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2510
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 82
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 340
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 26
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8167
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 103
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 966
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 475
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2936
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1089
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 27
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 29940
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 472
  bin: 4.75e1
  variant carriers: 0
num of homozygotes: 0
population: East Asian
population: European (Non-Finnish)
population: African
population: Latino
population: Other
population: European (Finnish)
population: South Asian
reference allele: C
site quality: FS
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: MQ
site quality: ReadPosRankSum
site quality: QD
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: DP

9-139904966-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904966
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904966
    reference: chr 9
allele count: 1
allele frequency: 2.345215759849906e-5
allele num: 42640
alternate allele: A
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.*3329+106C>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.6171+106C>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.6174+106C>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: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.*4C>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.*266+106C>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: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+106C>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.6174+106C>T
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: 3' UTR
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 102
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 28611
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8775
  bin: 2.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 387
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1707
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6435
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 52
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2513
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 23
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9344
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 45
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 203
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 37
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6649
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 528
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 29060
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1501
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 521
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 108
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1163
  bin: 6.75e1
  variant carriers: 0
num of homozygotes: 0
population: East Asian
population: South Asian
population: African
population: Latino
population: European (Non-Finnish)
population: European (Finnish)
population: Other
reference allele: G
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: MQ
site quality: MQRankSum
site quality: VQSLOD
site quality: ReadPosRankSum
site quality: FS
site quality: QD
site quality: DP
site quality: BaseQRankSum

9-139904971-C-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904971
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904971
    reference: chr 9
allele count: 1
allele frequency: 1.883097318469418e-5
allele num: 53104
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.6171+101G>C
  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.*3329+101G>C
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: stop_lost
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.4324G>C
  hgvsp: ENSP00000420084.1:p.Ter1442SerextTer42
  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.6174+101G>C
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+101G>C
  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.6174+101G>C
  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.*266+101G>C
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: stop lost
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 147
  bin: 3.75e1
  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: 6
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8412
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2187
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2364
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 25
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4652
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 677
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13944
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 59
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 39
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 25835
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 26859
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3092
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12503
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4865
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 846
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 528
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 62
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 420
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 195
  bin: 8.25e1
  variant carriers: 0
hgvs: p.Ter1442SerextTer42
num of homozygotes: 0
population: Other
population: South Asian
population: European (Finnish)
population: European (Non-Finnish)
population: Latino
population: East Asian
population: African
reference allele: C
site quality: VQSLOD
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: QD
site quality: DP
site quality: MQRankSum
site quality: FS
site quality: ClippingRankSum
site quality: MQ
site quality: InbreedingCoeff

9-139904973-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904973
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904973
    reference: chr 9
allele count: 1
allele frequency: 1.732801940738174e-5
allele num: 57710
alternate allele: A
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.*266+99C>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.6174+99C>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.6174+99C>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: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+99C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.4322C>T
  hgvsp: ENST00000479446.1:c.4322C>T(p.%3D)
  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.6171+99C>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.*3329+99C>T
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 39
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2751
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16434
  bin: 2.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 4000
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 24162
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 192
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 24
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2175
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 861
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7804
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 68
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 514
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 25267
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4307
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2510
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 369
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 880
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1379
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2258
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2890
  bin: 2.75e1
  variant carriers: 0
hgvs: p.Pro1441Pro
num of homozygotes: 0
population: European (Finnish)
population: Latino
population: South Asian
population: African
population: European (Non-Finnish)
population: East Asian
population: Other
reference allele: G
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: QD
site quality: ClippingRankSum
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: DP
site quality: MQ
site quality: FS
site quality: BaseQRankSum

http://identifiers.org/exac.variant/9-139904981-C-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904981
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904981
    reference: chr 9
allele count: 1
allele frequency: 1.338114863779907e-5
allele num: 74732
alternate allele: A
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.*3329+91G>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.6174+91G>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.*266+91G>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.6171+91G>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: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+91G>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.6174+91G>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.4314G>T
  hgvsp: ENSP00000420084.1:p.Ala1439Ser
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4669
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 108
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2072
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 48
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 23874
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 355
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17798
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5437
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2722
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 28
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1742
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2862
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 140
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 962
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 351
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 22381
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 474
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3502
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 865
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 503
  bin: 2.5e0
  variant carriers: 0
hgvs: p.Ala1439Ser
num of homozygotes: 0
population: African
population: European (Non-Finnish)
population: Other
population: European (Finnish)
population: South Asian
population: Latino
population: East Asian
reference allele: C
site quality: MQRankSum
site quality: DP
site quality: VQSLOD
site quality: MQ
site quality: QD
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: FS
site quality: ClippingRankSum
site quality: ReadPosRankSum

9-139904987-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904987
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904987
    reference: chr 9
allele count: 2
allele frequency: 2.304731614003549e-5
allele num: 86778
alternate allele: T
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.6174+85G>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.*266+85G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.4308G>A
  hgvsp: ENSP00000420084.1:p.Gly1437Arg
  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.6171+85G>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.*3329+85G>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: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+85G>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.6174+85G>A
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12937
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2475
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6127
  bin: 2.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 2192
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3686
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 156
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 485
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 21
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1601
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29322
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 61
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 27
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1163
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 613
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1253
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2257
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 993
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 276
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 212
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 231
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13428
  bin: 2.25e1
  variant carriers: 0
hgvs: p.Gly1437Arg
num of homozygotes: 0
population: European (Finnish)
population: South Asian
population: African
population: Latino
population: East Asian
population: Other
population: European (Non-Finnish)
reference allele: C
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: FS
site quality: QD
site quality: VQSLOD
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: MQ
site quality: MQRankSum
site quality: DP

9-139904989-G-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904989
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904989
    reference: chr 9
allele count: 1
allele frequency: 1.111358079573239e-5
allele num: 89980
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.4306C>G
  hgvsp: ENSP00000420084.1:p.Pro1436Arg
  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.*3329+83C>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.6171+83C>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.*266+83C>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.6174+83C>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: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+83C>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.6174+83C>G
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 21
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3266
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 526
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 65
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 30704
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2033
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11546
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6604
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2680
  bin: 3.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1490
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 30
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 165
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 493
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12005
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 977
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1229
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 310
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 230
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4768
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 260
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2119
  bin: 7.5e0
  variant carriers: 0
hgvs: p.Pro1436Arg
num of homozygotes: 0
population: Latino
population: Other
population: East Asian
population: South Asian
population: European (Finnish)
population: African
population: European (Non-Finnish)
reference allele: G
site quality: InbreedingCoeff
site quality: MQ
site quality: FS
site quality: ClippingRankSum
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: QD
site quality: BaseQRankSum
site quality: VQSLOD
site quality: DP

9-139904992-T-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904992
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904992
    reference: chr 9
allele count: 1
allele frequency: 1.060355431140518e-5
allele num: 94308
alternate allele: G
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.*266+80A>C
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+80A>C
  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.*3329+80A>C
  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.6171+80A>C
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.4303A>C
  hgvsp: ENSP00000420084.1:p.Glu1435Ala
  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.6174+80A>C
  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.6174+80A>C
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 589
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 76
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7229
  bin: 2.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9758
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32458
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 19
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1859
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 37
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3046
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1248
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2691
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 198
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 272
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1502
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 857
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 504
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 717
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 217
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1183
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1322
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 434
  bin: 5.25e1
  variant carriers: 0
hgvs: p.Glu1435Ala
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: T
site quality: DP
site quality: MQ
site quality: FS
site quality: MQRankSum
site quality: ClippingRankSum
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: QD

9-139904997-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904997
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904997
    reference: chr 9
allele count: 11
allele frequency: 1.098023557596327e-4
allele num: 100180
alternate allele: T
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.*266+75G>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.6174+75G>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.*3329+75G>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.6174+75G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.4298G>A
  hgvsp: ENST00000479446.1:c.4298G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+75G>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.6171+75G>A
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 254
  bin: 4.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 7235
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1927
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3710
  bin: 3.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 1687
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 96
  bin: 4.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 884
  bin: 1.75e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 7.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 684
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 34585
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 35
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8192
  bin: 2.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 24
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 167
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 35140
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1701
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 392
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1513
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1699
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 185
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 658
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 876
  bin: 2.75e1
  variant carriers: 0
hgvs: p.Glu1433Glu
num of homozygotes: 0
population: African
population: European (Non-Finnish)
population: South Asian
population: East Asian
population: Other
population: Latino
population: European (Finnish)
reference allele: C
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: FS
site quality: DP
site quality: VQSLOD
site quality: MQ
site quality: ClippingRankSum
site quality: QD

9-139904999-C-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904999
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904999
    reference: chr 9
allele count: 4
allele frequency: 3.923799807733809e-5
allele num: 101942
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.6174+73G>C
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+73G>C
  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.6171+73G>C
  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.6174+73G>C
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.4296G>C
  hgvsp: ENSP00000420084.1:p.Glu1433Gln
  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.*3329+73G>C
  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.*266+73G>C
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 6456
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1661
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1685
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 107
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8431
  bin: 2.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 732
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 35269
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3918
  bin: 3.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 767
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 24
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 269
  bin: 4.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 39
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 285
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 36125
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 122
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 317
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 287
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1550
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 150
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6683
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 368
  bin: 4.75e1
  variant carriers: 0
hgvs: p.Glu1433Gln
num of homozygotes: 0
population: African
population: Other
population: European (Non-Finnish)
population: East Asian
population: South Asian
population: Latino
population: European (Finnish)
reference allele: C
site quality: ClippingRankSum
site quality: MQ
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: FS
site quality: BaseQRankSum
site quality: DP
site quality: QD

9-139904999-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139904999
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139904999
    reference: chr 9
allele count: 1
allele frequency: 9.809499519334523e-6
allele num: 101942
alternate allele: T
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.*3329+73G>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.6174+73G>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.6171+73G>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.*266+73G>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: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+73G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.4296G>A
  hgvsp: ENSP00000420084.1:p.Glu1433Lys
  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.6174+73G>A
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 7.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 35269
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 767
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8431
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1661
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1685
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3918
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 24
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6456
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 107
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 269
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 732
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 39
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 745
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 875
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 368
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 313
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6683
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 36125
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 167
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 603
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 122
  bin: 1.25e1
  variant carriers: 0
hgvs: p.Glu1433Lys
num of homozygotes: 0
population: East Asian
population: Other
population: European (Non-Finnish)
population: Latino
population: African
population: South Asian
population: European (Finnish)
reference allele: C
site quality: MQ
site quality: DP
site quality: MQRankSum
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: FS
site quality: ReadPosRankSum
site quality: QD
site quality: BaseQRankSum

9-139905002-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139905002
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139905002
    reference: chr 9
allele count: 1
allele frequency: 9.584970765839164e-6
allele num: 104330
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+70G>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.6171+70G>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.*3329+70G>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.6174+70G>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.6174+70G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.4293G>A
  hgvsp: ENSP00000420084.1:p.Val1432Met
  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.*266+70G>A
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1585
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1396
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 36038
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 41
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 668
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 26
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 111
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5422
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8835
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 305
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4176
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 795
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 9
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 271
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5606
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 492
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 669
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 296
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 37282
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 674
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 130
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 334
  bin: 4.75e1
  variant carriers: 0
hgvs: p.Val1432Met
num of homozygotes: 0
population: East Asian
population: European (Finnish)
population: South Asian
population: African
population: Latino
population: European (Non-Finnish)
population: Other
reference allele: C
site quality: MQ
site quality: QD
site quality: FS
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: MQRankSum
site quality: ClippingRankSum
site quality: DP
site quality: BaseQRankSum
site quality: ReadPosRankSum

9-139905009-G-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139905009
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139905009
    reference: chr 9
allele count: 0
allele frequency: 0.0e0
allele num: 108134
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.4286C>A
  hgvsp: ENST00000479446.1:c.4286C>A(p.%3D)
  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.*266+63C>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.*3329+63C>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.6174+63C>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: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+63C>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.6174+63C>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.6171+63C>A
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: synonymous
filter: AC_Adj0_Filter
genotype depth: GenotypeDepth
  all individuals: 4664
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 37051
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3800
  bin: 7.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 364
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1458
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 50
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 867
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 31
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 929
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 128
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9631
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 500
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 252
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 956
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 151
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 39299
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 259
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 269
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1443
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 263
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 310
  bin: 9.25e1
  variant carriers: 0
hgvs: p.Ala1429Ala
num of homozygotes: 0
population: Latino
population: European (Finnish)
population: African
population: South Asian
population: East Asian
population: Other
population: European (Non-Finnish)
reference allele: G
site quality: MQ
site quality: DP
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: FS
site quality: QD
site quality: VQSLOD
site quality: MQRankSum
site quality: BaseQRankSum
site quality: ReadPosRankSum

9-139905010-GC-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139905010
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139905009
    reference: chr 9
allele count: 1
allele frequency: 9.229860444510079e-6
allele num: 108344
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.6174+61delG
  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.*3329+61delG
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: frameshift_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.4284delG
  hgvsp: ENSP00000420084.1:p.Ala1429ProfsTer76
  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.6171+61delG
  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.*266+61delG
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+61delG
  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.6174+61delG
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: frameshift
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 507
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 36
  bin: 5.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1435
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 54
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 856
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 36997
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4690
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9734
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3699
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 386
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 949
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 126
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 260
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 449
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1956
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 308
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 118
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 289
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 172
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 959
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 285
  bin: 5.25e1
  variant carriers: 0
hgvs: p.Ala1429ProfsTer76
num of homozygotes: 0
population: South Asian
population: Other
population: East Asian
population: European (Non-Finnish)
population: European (Finnish)
population: African
population: Latino
reference allele: GC
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: MQRankSum
site quality: FS
site quality: MQ
site quality: DP
site quality: ClippingRankSum
site quality: QD
site quality: BaseQRankSum
site quality: ReadPosRankSum

http://identifiers.org/exac.variant/9-139905015-A-AC
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139905015
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139905016
    reference: chr 9
allele count: 1
allele frequency: 9.066676337788093e-6
allele num: 110294
alternate allele: AC
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.*266+56dupG
  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.6171+56dupG
  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.6174+56dupG
  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.*3329+56dupG
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: frameshift_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.4279dupG
  hgvsp: ENSP00000420084.1:p.Gly1428TrpfsTer443
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+56dupG
  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.6174+56dupG
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: frameshift
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 2857
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1365
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 702
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5180
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 65
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 36497
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 383
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 458
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 161
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1067
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 49
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10777
  bin: 2.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 321
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 331
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 287
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2041
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1367
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 348
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2936
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 122
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 191
  bin: 2.5e0
  variant carriers: 0
hgvs: p.Gly1428TrpfsTer443
num of homozygotes: 0
population: African
population: South Asian
population: East Asian
population: Latino
population: Other
population: European (Non-Finnish)
population: European (Finnish)
reference allele: A
site quality: ReadPosRankSum
site quality: QD
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: FS
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: DP
site quality: MQRankSum
site quality: MQ

http://identifiers.org/exac.variant/9-139905015-AC-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139905015
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139905014
    reference: chr 9
allele count: 8
allele frequency: 7.253341070230474e-5
allele num: 110294
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: frameshift_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.4279delG
  hgvsp: ENSP00000420084.1:p.Gly1427ValfsTer78
  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.*266+56delG
  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.6174+56delG
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+56delG
  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.6171+56delG
  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.6174+56delG
  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.*3329+56delG
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: frameshift
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 383
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1067
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 8.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5180
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 702
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 65
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 6.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1365
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2857
  bin: 7.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 458
  bin: 4.25e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 49
  bin: 5.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 10777
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 161
  bin: 4.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 36497
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2041
  bin: 7.25e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 40015
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1367
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 236
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2936
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 96
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 321
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 122
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 348
  bin: 3.25e1
  variant carriers: 0
hgvs: p.Gly1427ValfsTer78
num of homozygotes: 0
population: South Asian
population: African
population: European (Finnish)
population: Latino
population: Other
population: East Asian
population: European (Non-Finnish)
reference allele: AC
site quality: MQRankSum
site quality: VQSLOD
site quality: ReadPosRankSum
site quality: MQ
site quality: BaseQRankSum
site quality: DP
site quality: FS
site quality: ClippingRankSum
site quality: QD
site quality: InbreedingCoeff

9-139905016-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139905016
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139905016
    reference: chr 9
allele count: 1
allele frequency: 9.03864926425395e-6
allele num: 110636
alternate allele: T
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.*266+56G>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.6171+56G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.4279G>A
  hgvsp: ENSP00000420084.1:p.Gly1427Asp
  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.*3329+56G>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.6174+56G>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: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+56G>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.6174+56G>A
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: missense
filter: VQSRTrancheSNP99.60to99.80
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 7.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 157
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 676
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 68
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1361
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5234
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2749
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10938
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 41
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 359
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 36484
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 441
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1062
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 995
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 40101
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 321
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 375
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 342
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 85
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 353
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 148
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1330
  bin: 7.5e0
  variant carriers: 0
hgvs: p.Gly1427Asp
num of homozygotes: 0
population: Latino
population: East Asian
population: Other
population: European (Finnish)
population: African
population: European (Non-Finnish)
population: South Asian
reference allele: C
site quality: ClippingRankSum
site quality: FS
site quality: MQ
site quality: InbreedingCoeff
site quality: QD
site quality: MQRankSum
site quality: VQSLOD
site quality: ReadPosRankSum
site quality: BaseQRankSum
site quality: DP

9-139905021-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139905021
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139905021
    reference: chr 9
allele count: 1
allele frequency: 8.874689385871495e-6
allele num: 112680
alternate allele: T
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.*3329+51G>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.6174+51G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.4274G>A
  hgvsp: ENST00000479446.1:c.4274G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+51G>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.6171+51G>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.*266+51G>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.6174+51G>A
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 2042
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1082
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 36
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 163
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 54
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 37005
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 194
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1360
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11440
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 494
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 385
  bin: 4.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5493
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 109
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 102
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1315
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2123
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 155
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 41715
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 359
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 7348
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 87
  bin: 1.75e1
  variant carriers: 0
hgvs: p.Gln1425Gln
num of homozygotes: 0
population: European (Non-Finnish)
population: European (Finnish)
population: East Asian
population: Other
population: Latino
population: African
population: South Asian
reference allele: C
site quality: InbreedingCoeff
site quality: FS
site quality: QD
site quality: BaseQRankSum
site quality: DP
site quality: VQSLOD
site quality: ReadPosRankSum
site quality: MQ
site quality: MQRankSum
site quality: ClippingRankSum

9-139905027-C-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139905027
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139905027
    reference: chr 9
allele count: 273
allele frequency: 2.390919759681911e-3
allele num: 114182
alternate allele: G
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.*266+45G>C
  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.6174+45G>C
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.4268G>C
  hgvsp: ENSP00000420084.1:p.Gln1423His
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+45G>C
  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.6171+45G>C
  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.*3329+45G>C
  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.6174+45G>C
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 74
  bin: 5.25e1
  variant carriers: 26
genotype depth: GenotypeDepth
  all individuals: 361
  bin: 1.25e1
  variant carriers: 5
genotype depth: GenotypeDepth
  all individuals: 30
  bin: 7.25e1
  variant carriers: 23
genotype depth: GenotypeDepth
  all individuals: 168
  bin: 4.75e1
  variant carriers: 12
genotype depth: GenotypeDepth
  all individuals: 58
  bin: 9.75e1
  variant carriers: 51
genotype depth: GenotypeDepth
  all individuals: 37282
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5580
  bin: 3.25e1
  variant carriers: 8
genotype depth: GenotypeDepth
  all individuals: 410
  bin: 4.25e1
  variant carriers: 13
genotype depth: GenotypeDepth
  all individuals: 1268
  bin: 2.5e0
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 1115
  bin: 3.75e1
  variant carriers: 13
genotype depth: GenotypeDepth
  all individuals: 129
  bin: 1.75e1
  variant carriers: 4
genotype depth: GenotypeDepth
  all individuals: 20
  bin: 7.75e1
  variant carriers: 17
genotype depth: GenotypeDepth
  all individuals: 11729
  bin: 2.75e1
  variant carriers: 8
genotype depth: GenotypeDepth
  all individuals: 26
  bin: 8.25e1
  variant carriers: 22
genotype depth: GenotypeDepth
  all individuals: 1535
  bin: 7.5e0
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 29
  bin: 6.25e1
  variant carriers: 17
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 8.75e1
  variant carriers: 6
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 6.75e1
  variant carriers: 16
genotype depth: GenotypeDepth
  all individuals: 54
  bin: 5.75e1
  variant carriers: 17
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 9.25e1
  variant carriers: 14
genotype quality: GenotypeQuality
  all individuals: 7474
  bin: 6.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 79
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 130
  bin: 2.75e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 56
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 350
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 116
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 38
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 59
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 51
  bin: 5.25e1
  variant carriers: 0
hgvs: p.Gln1423His
num of homozygotes: 1
population: Other
population: European (Non-Finnish)
population: African
population: East Asian
population: Latino
population: European (Finnish)
population: South Asian
reference allele: C
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: FS
site quality: InbreedingCoeff
site quality: MQ
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: MQRankSum
site quality: QD
site quality: DP

9-139905027-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139905027
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139905027
    reference: chr 9
allele count: 2
allele frequency: 1.751589567532536e-5
allele num: 114182
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.6171+45G>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.*266+45G>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.*3329+45G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.4268G>A
  hgvsp: ENST00000479446.1:c.4268G>A(p.%3D)
  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.6174+45G>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.6174+45G>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: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+45G>A
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 410
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1535
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 54
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 26
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 361
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 168
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1268
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11729
  bin: 2.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 5580
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 129
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 58
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 30
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 74
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1115
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 37282
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 59
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 116
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 79
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2155
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1231
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 643
  bin: 9.75e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 38
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7474
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1034
  bin: 8.25e1
  variant carriers: 0
hgvs: p.Gln1423Gln
num of homozygotes: 0
population: South Asian
population: East Asian
population: Other
population: European (Finnish)
population: European (Non-Finnish)
population: Latino
population: African
reference allele: C
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: QD
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: MQ
site quality: DP
site quality: FS
site quality: BaseQRankSum

9-139905030-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139905030
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139905030
    reference: chr 9
allele count: 1
allele frequency: 8.72280665026779e-6
allele num: 114642
alternate allele: A
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.*3329+42C>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.6174+42C>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.6171+42C>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.6174+42C>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.*266+42C>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: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+42C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.4265C>T
  hgvsp: ENST00000479446.1:c.4265C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1433
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 116
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 61
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 37416
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1179
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 177
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 329
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1156
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 419
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11870
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5703
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 423
  bin: 9.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 369
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2175
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 52
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 53
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1486
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 42
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 42792
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 73
  bin: 2.5e0
  variant carriers: 0
hgvs: p.Gly1422Gly
num of homozygotes: 0
population: South Asian
population: European (Finnish)
population: East Asian
population: European (Non-Finnish)
population: Latino
population: African
population: Other
reference allele: G
site quality: VQSLOD
site quality: BaseQRankSum
site quality: QD
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: FS
site quality: ReadPosRankSum
site quality: ClippingRankSum
site quality: DP
site quality: MQ

9-139905034-A-ACCCCACCCAGG
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139905034
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139905045
    reference: chr 9
allele count: 1
allele frequency: 8.695652173913043e-6
allele num: 115000
alternate allele: ACCCCACCCAGG
annotation: Annotation
  canonical: false
  consequence: frameshift_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsp: ENSP00000420084.1:p.Val1421AlafsTer5
  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
  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
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: 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: 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: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000463603
  gene symbol: ABCA2
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: frameshift
filter: VQSRTrancheINDEL99.00to99.50
genotype depth: GenotypeDepth
  all individuals: 79
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1354
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 182
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1047
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 65
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 37365
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5767
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11976
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 454
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 325
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 100
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1201
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 23
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 26
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 9.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 993
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 106
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7554
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 63
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 363
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 129
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1042
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 160
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1881
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 404
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1352
  bin: 2.25e1
  variant carriers: 0
hgvs: p.Val1421AlafsTer5
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: A
site quality: VQSLOD
site quality: QD
site quality: MQRankSum
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: MQ
site quality: BaseQRankSum
site quality: FS
site quality: DP

9-139905036-C-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139905036
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139905036
    reference: chr 9
allele count: 1
allele frequency: 8.670921198668147e-6
allele num: 115328
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+36G>C
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.4259G>C
  hgvsp: ENST00000479446.1:c.4259G>C(p.%3D)
  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.6174+36G>C
  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.6171+36G>C
  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.6174+36G>C
  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.*3329+36G>C
  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.*266+36G>C
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: synonymous
filter: VQSRTrancheSNP99.60to99.80
genotype depth: GenotypeDepth
  all individuals: 423
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1191
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 308
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 37428
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12087
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 94
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1005
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 58
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 50
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 179
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5805
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1324
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2191
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 60
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 43054
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1056
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1329
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 71
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 49
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 25
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 111
  bin: 2.75e1
  variant carriers: 0
hgvs: p.Gly1420Gly
num of homozygotes: 0
population: European (Finnish)
population: European (Non-Finnish)
population: Latino
population: African
population: South Asian
population: East Asian
population: Other
reference allele: C
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: FS
site quality: DP
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: QD
site quality: VQSLOD
site quality: MQ
site quality: MQRankSum

9-139905039-A-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139905039
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139905039
    reference: chr 9
allele count: 1
allele frequency: 8.628425484917513e-6
allele num: 115896
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.6171+33T>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.4256T>A
  hgvsp: ENST00000479446.1:c.4256T>A(p.%3D)
  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.*266+33T>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.6174+33T>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.*3329+33T>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: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+33T>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.6174+33T>A
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5827
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1201
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 62
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 61
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 878
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1219
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12217
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 37599
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 273
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 183
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 428
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 25
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 370
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 469
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 101
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 23
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 412
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 85
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 32
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2207
  bin: 7.25e1
  variant carriers: 0
hgvs: p.Gly1419Gly
num of homozygotes: 0
population: European (Finnish)
population: European (Non-Finnish)
population: South Asian
population: Other
population: East Asian
population: African
population: Latino
reference allele: A
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: MQRankSum
site quality: DP
site quality: QD
site quality: FS
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: MQ

9-139905048-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139905048
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139905048
    reference: chr 9
allele count: 52
allele frequency: 4.460150272755343e-4
allele num: 116588
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+24G>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.*3329+24G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: stop_gained
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.4247G>A
  hgvsp: ENSP00000420084.1:p.Trp1416Ter
  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.*266+24G>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.6174+24G>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.6174+24G>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.6171+24G>A
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: stop gained
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 53
  bin: 5.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 651
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 201
  bin: 1.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 12
  bin: 7.25e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 9.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 21
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1210
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5854
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 19
  bin: 6.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1196
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12316
  bin: 2.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 37877
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 422
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 180
  bin: 4.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 49
  bin: 9.75e1
  variant carriers: 38
genotype depth: GenotypeDepth
  all individuals: 60
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18
  bin: 6.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 86
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 19
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1179
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 43812
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 31
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1911
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 40
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 59
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 39
  bin: 2.5e0
  variant carriers: 0
hgvs: p.Trp1416Ter
num of homozygotes: 1
population: East Asian
population: Latino
population: South Asian
population: European (Finnish)
population: African
population: Other
population: European (Non-Finnish)
reference allele: C
site quality: VQSLOD
site quality: BaseQRankSum
site quality: FS
site quality: MQRankSum
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: DP
site quality: MQ
site quality: QD

9-139905057-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139905057
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139905057
    reference: chr 9
allele count: 39
allele frequency: 3.32707729056475e-4
allele num: 117220
alternate allele: G
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.*266+15T>C
  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.6174+15T>C
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+15T>C
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.4238T>C
  hgvsp: ENST00000479446.1:c.4238T>C(p.%3D)
  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.6174+15T>C
  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.6171+15T>C
  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.*3329+15T>C
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 9.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 61
  bin: 5.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 423
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 26
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 179
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 132
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 53
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 536
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1065
  bin: 7.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5864
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12
  bin: 7.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 20
  bin: 6.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 21
  bin: 6.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 38150
  bin: 2.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 12367
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1210
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 80
  bin: 9.75e1
  variant carriers: 32
genotype quality: GenotypeQuality
  all individuals: 47
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 30
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2217
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 54
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 375
  bin: 9.25e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1913
  bin: 7.75e1
  variant carriers: 0
hgvs: p.His1413His
num of homozygotes: 0
population: Other
population: South Asian
population: European (Non-Finnish)
population: Latino
population: African
population: East Asian
population: European (Finnish)
reference allele: A
site quality: DP
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: MQ
site quality: FS
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: QD
site quality: VQSLOD

9-139905058-T-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139905058
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139905058
    reference: chr 9
allele count: 1
allele frequency: 8.530094172239662e-6
allele num: 117232
alternate allele: A
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.*266+14A>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.6171+14A>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: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+14A>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.6174+14A>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.6174+14A>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.4237A>T
  hgvsp: ENSP00000420084.1:p.His1413Leu
  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.*3329+14A>T
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 53
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1062
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 30
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 530
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 179
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 21
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12369
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20
  bin: 6.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1210
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5865
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 131
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 80
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 424
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 61
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 38155
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 26
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7764
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 53
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 44132
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 45
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 505
  bin: 7.5e0
  variant carriers: 0
hgvs: p.His1413Leu
num of homozygotes: 0
population: East Asian
population: Latino
population: European (Non-Finnish)
population: African
population: Other
population: European (Finnish)
population: South Asian
reference allele: T
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: FS
site quality: QD
site quality: MQ
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: DP
site quality: ClippingRankSum
site quality: BaseQRankSum

http://identifiers.org/exac.variant/9-139905060-C-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139905060
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139905060
    reference: chr 9
allele count: 1
allele frequency: 8.524131817174421e-6
allele num: 117314
alternate allele: A
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.6174+12G>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.6171+12G>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.6174+12G>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.*266+12G>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.*3329+12G>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.4235G>T
  hgvsp: ENST00000479446.1:c.4235G>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl transcript: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.162+12G>T
  variant of: http://identifiers.org/hgnc/32
canonical: false
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 423
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 21
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 510
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1212
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 179
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 137
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 38168
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 30
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 81
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1050
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 61
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5866
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12387
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 53
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 14
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7766
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 558
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 1068
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 56
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 29
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2216
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 29
  bin: 2.5e0
  variant carriers: 0
hgvs: p.Gly1412Gly
num of homozygotes: 0
population: African
population: European (Non-Finnish)
population: Latino
population: Other
population: European (Finnish)
population: South Asian
population: East Asian
reference allele: C
site quality: ReadPosRankSum
site quality: DP
site quality: MQ
site quality: QD
site quality: MQRankSum
site quality: VQSLOD
site quality: BaseQRankSum
site quality: FS
site quality: ClippingRankSum
site quality: InbreedingCoeff

9-139905086-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139905086
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139905086
    reference: chr 9
allele count: 1
allele frequency: 8.457660949287865e-6
allele num: 118236
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.6157G>A
  hgvsp: ENSP00000360666.3:p.Glu2053Lys
  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: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.*252G>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: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.*3315G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.4209G>A
  hgvsp: ENSP00000420084.1:p.Glu1404Lys
  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: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.148G>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.6160G>A
  hgvsp: ENSP00000344155.6:p.Glu2054Lys
  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.6160G>A
  hgvsp: ENSP00000265662.5:p.Glu2054Lys
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: VQSRTrancheSNP99.80to99.90
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 485
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 61
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12455
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 424
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 38580
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1211
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 750
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 53
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 81
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 103
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5883
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 21
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 179
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 24
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 750
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1072
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 34
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 37
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 465
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 20
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 18
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7799
  bin: 6.75e1
  variant carriers: 0
hgvs: p.Glu2054Lys
num of homozygotes: 0
population: African
population: Other
population: European (Finnish)
population: Latino
population: South Asian
population: East Asian
population: European (Non-Finnish)
reference allele: C
site quality: DP
site quality: BaseQRankSum
site quality: FS
site quality: ReadPosRankSum
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: QD
site quality: VQSLOD
site quality: MQ

9-139905107-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139905107
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139905107
    reference: chr 9
allele count: 5
allele frequency: 4.215282929790248e-5
allele num: 118616
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.4188G>A
  hgvsp: ENSP00000420084.1:p.Asp1397Asn
  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: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.127G>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.6139G>A
  hgvsp: ENSP00000344155.6:p.Asp2047Asn
  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: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.*231G>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.6139G>A
  hgvsp: ENSP00000265662.5:p.Asp2047Asn
  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.6136G>A
  hgvsp: ENSP00000360666.3:p.Asp2046Asn
  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: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.*3294G>A
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 578
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5887
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 58
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 53
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 180
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 85
  bin: 9.75e1
  variant carriers: 4
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 8.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 61
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 506
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 111
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 38688
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1211
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12487
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 424
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 21
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 44713
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7801
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 482
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 31
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2225
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 375
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 37
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 32
  bin: 2.5e0
  variant carriers: 0
hgvs: p.Asp2047Asn
num of homozygotes: 0
population: East Asian
population: European (Finnish)
population: Other
population: Latino
population: African
population: European (Non-Finnish)
population: South Asian
reference allele: C
site quality: MQ
site quality: VQSLOD
site quality: FS
site quality: DP
site quality: QD
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: ClippingRankSum

9-139905108-G-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139905108
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139905108
    reference: chr 9
allele count: 1
allele frequency: 8.429286713758282e-6
allele num: 118634
alternate allele: C
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.6138C>G
  hgvsp: ENST00000341511.6:c.6138C>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: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.4187C>G
  hgvsp: ENST00000479446.1:c.4187C>G(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: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.*230C>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: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.126C>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: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.*3293C>G
  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.6135C>G
  hgvsp: ENST00000371605.3:c.6135C>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.6138C>G
  hgvsp: ENST00000265662.5:c.6138C>G(p.%3D)
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 82
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 53
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 58
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 179
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 517
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 112
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 61
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 38698
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 424
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12483
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5891
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 569
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 21
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 21
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1212
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 38
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 498
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2225
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 15
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7803
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 31
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 44753
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 26
  bin: 2.5e0
  variant carriers: 0
hgvs: p.Ala2046Ala
num of homozygotes: 0
population: African
population: South Asian
population: East Asian
population: European (Non-Finnish)
population: European (Finnish)
population: Latino
population: Other
reference allele: G
site quality: DP
site quality: MQ
site quality: BaseQRankSum
site quality: FS
site quality: VQSLOD
site quality: QD
site quality: MQRankSum
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: ReadPosRankSum

9-139905111-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139905111
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139905111
    reference: chr 9
allele count: 4
allele frequency: 3.371146358319146e-5
allele num: 118654
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.6135C>T
  hgvsp: ENST00000265662.5:c.6135C>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.6132C>T
  hgvsp: ENST00000371605.3:c.6132C>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: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.*227C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.4184C>T
  hgvsp: ENST00000479446.1:c.4184C>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: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.123C>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.6135C>T
  hgvsp: ENST00000341511.6:c.6135C>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: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.*3290C>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 5891
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 38675
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 8.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 180
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 83
  bin: 9.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 561
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 21
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 120
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 19
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 53
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 67
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 518
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12497
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 424
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 12
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1211
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 61
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 15
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 420
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 14
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 31
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 585
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 375
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 44724
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 501
  bin: 7.5e0
  variant carriers: 0
hgvs: p.Asp2045Asp
num of homozygotes: 0
population: European (Non-Finnish)
population: European (Finnish)
population: Latino
population: Other
population: African
population: East Asian
population: South Asian
reference allele: G
site quality: ReadPosRankSum
site quality: BaseQRankSum
site quality: VQSLOD
site quality: FS
site quality: DP
site quality: MQRankSum
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: QD
site quality: MQ

9-139905117-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139905117
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139905117
    reference: chr 9
allele count: 29
allele frequency: 2.443092786979158e-4
allele num: 118702
alternate allele: T
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.6129G>A
  hgvsp: ENST00000341511.6:c.6129G>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.6129G>A
  hgvsp: ENST00000265662.5:c.6129G>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: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.*3284G>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.6126G>A
  hgvsp: ENST00000371605.3:c.6126G>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: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.117G>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: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.*221G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.4178G>A
  hgvsp: ENST00000479446.1:c.4178G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 182
  bin: 4.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1218
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 540
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 38610
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 90
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 23
  bin: 6.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 65
  bin: 5.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 504
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 103
  bin: 9.75e1
  variant carriers: 22
genotype depth: GenotypeDepth
  all individuals: 53
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 158
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 5899
  bin: 3.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 12479
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 19
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 8.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 424
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 28
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 46
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2220
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 596
  bin: 9.75e1
  variant carriers: 29
genotype quality: GenotypeQuality
  all individuals: 44658
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 23
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1915
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 19
  bin: 1.25e1
  variant carriers: 0
hgvs: p.Arg2043Arg
num of homozygotes: 0
population: East Asian
population: Other
population: European (Non-Finnish)
population: South Asian
population: African
population: Latino
population: European (Finnish)
reference allele: C
site quality: MQRankSum
site quality: FS
site quality: QD
site quality: VQSLOD
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: DP
site quality: BaseQRankSum
site quality: MQ
site quality: ReadPosRankSum

9-139905118-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139905118
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139905118
    reference: chr 9
allele count: 6
allele frequency: 5.055015417797025e-5
allele num: 118694
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.6125G>A
  hgvsp: ENSP00000360666.3:p.Arg2042Gln
  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.6128G>A
  hgvsp: ENSP00000344155.6:p.Arg2043Gln
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.4177G>A
  hgvsp: ENSP00000420084.1:p.Arg1393Gln
  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: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.116G>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.6128G>A
  hgvsp: ENSP00000265662.5:p.Arg2043Gln
  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: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.*220G>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: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.*3283G>A
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 53
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 428
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 63
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 157
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 505
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5918
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12487
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 38584
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 538
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 182
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 22
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1227
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 85
  bin: 9.75e1
  variant carriers: 4
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 9.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 19
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 41
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 574
  bin: 9.75e1
  variant carriers: 5
genotype quality: GenotypeQuality
  all individuals: 568
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 30
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 25
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 44644
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 15
  bin: 4.25e1
  variant carriers: 0
hgvs: p.Arg2043Gln
num of homozygotes: 1
population: Other
population: Latino
population: European (Non-Finnish)
population: South Asian
population: African
population: East Asian
population: European (Finnish)
reference allele: C
site quality: FS
site quality: ReadPosRankSum
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: ClippingRankSum
site quality: MQRankSum
site quality: DP
site quality: MQ
site quality: BaseQRankSum
site quality: QD

9-139905119-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139905119
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139905119
    reference: chr 9
allele count: 2
allele frequency: 1.684863189109044e-5
allele num: 118704
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.4176C>T
  hgvsp: ENSP00000420084.1:p.Arg1393Trp
  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.6124C>T
  hgvsp: ENSP00000360666.3:p.Arg2042Trp
  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.6127C>T
  hgvsp: ENSP00000344155.6:p.Arg2043Trp
  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.6127C>T
  hgvsp: ENSP00000265662.5:p.Arg2043Trp
  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: ENST00000463603
  gene symbol: ABCA2
  hgvsc: ENST00000463603.1:n.115C>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
hgvs: p.Arg2043Trp
num of homozygotes: 0
reference allele: G

GenotypeQuality
all individuals: 620
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 9544
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 303
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 4767
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 20
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 2211
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 41
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 546
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 120
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 170
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1718
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 525
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 805
bin: 6.75e1
variant carriers: 0

African
type: Population
allele count: 1
allele frequency: 2.398081534772182e-4
allele num: 4170
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 434
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 32836
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 4162
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1594
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5478
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10658
num of homozygotes: 0

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.21e-2

DP
type: SiteQuality
SIO_000300: 7.20923e5

MQRankSum
type: SiteQuality
SIO_000300: -4.7e-1

FS
type: SiteQuality
SIO_000300: 0.0e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.03e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -3.36e-1

VQSLOD
type: SiteQuality
SIO_000300: -1.601e0

QD
type: SiteQuality
SIO_000300: 5.29e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

BaseQRankSum
type: SiteQuality
SIO_000300: -3.36e-1

GenotypeQuality
all individuals: 29840
bin: 2.25e1
variant carriers: 15

GenotypeQuality
all individuals: 759
bin: 2.5e0
variant carriers: 3

GenotypeQuality
all individuals: 1515
bin: 1.25e1
variant carriers: 9

GenotypeQuality
all individuals: 447
bin: 5.25e1
variant carriers: 25

GenotypeQuality
all individuals: 1401
bin: 3.75e1
variant carriers: 14

GenotypeQuality
all individuals: 2329
bin: 1.75e1
variant carriers: 9

GenotypeQuality
all individuals: 2769
bin: 2.75e1
variant carriers: 8

GenotypeQuality
all individuals: 523
bin: 4.75e1
variant carriers: 28

GenotypeQuality
all individuals: 2734
bin: 3.25e1
variant carriers: 18

GenotypeQuality
all individuals: 86
bin: 8.25e1
variant carriers: 57

GenotypeQuality
all individuals: 136
bin: 7.75e1
variant carriers: 44

GenotypeQuality
all individuals: 66
bin: 9.25e1
variant carriers: 50

GenotypeQuality
all individuals: 1679
bin: 9.75e1
variant carriers: 1669

Latino
type: Population
allele count: 127
allele frequency: 2.48435054773083e-2
allele num: 5112
num of homozygotes: 1

European (Finnish)
type: Population
allele count: 29
allele frequency: 1.954177897574124e-2
allele num: 1484
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1386
allele frequency: 4.408957882682275e-2
allele num: 31436
num of homozygotes: 22

Other
type: Population
allele count: 16
allele frequency: 3.80952380952381e-2
allele num: 420
num of homozygotes: 2

African
type: Population
allele count: 36
allele frequency: 8.964143426294821e-3
allele num: 4016
num of homozygotes: 0

South Asian
type: Population
allele count: 194
allele frequency: 1.851498377552968e-2
allele num: 10478
num of homozygotes: 3

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 3866
num of homozygotes: 0

ReadPosRankSum
type: SiteQuality
SIO_000300: 3.15e-1

FS
type: SiteQuality
SIO_000300: 1.112e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -7.0e-4

BaseQRankSum
type: SiteQuality
SIO_000300: 9.1e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

MQRankSum
type: SiteQuality
SIO_000300: 1.43e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -1.96e-1

VQSLOD
type: SiteQuality
SIO_000300: 4.42e0

QD
type: SiteQuality
SIO_000300: 1.28e1

DP
type: SiteQuality
SIO_000300: 7.27089e5

GenotypeQuality
all individuals: 517
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 5599
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 153
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 12
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 25
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 114
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 2788
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 485
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 31174
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 8629
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2666
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 413
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 767
bin: 6.75e1
variant carriers: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 29266
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 386
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 4682
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1362
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 3728
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 2.609603340292275e-4
allele num: 3832
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10236
num of homozygotes: 0

BaseQRankSum
type: SiteQuality
SIO_000300: 1.88e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

VQSLOD
type: SiteQuality
SIO_000300: -1.802e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.42e-2

DP
type: SiteQuality
SIO_000300: 6.88428e5

ReadPosRankSum
type: SiteQuality
SIO_000300: -3.37e-1

MQRankSum
type: SiteQuality
SIO_000300: 0.0e0

ClippingRankSum
type: SiteQuality
SIO_000300: 4.04e-1

QD
type: SiteQuality
SIO_000300: 2.236e1

FS
type: SiteQuality
SIO_000300: 1.5761e1

GenotypeQuality
all individuals: 31799
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 8964
bin: 6.25e1
variant carriers: 0

GenotypeQuality
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bin: 5.25e1
variant carriers: 0

GenotypeQuality
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bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 5632
bin: 7.5e0
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GenotypeQuality
all individuals: 2174
bin: 1.75e1
variant carriers: 0

GenotypeQuality
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bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 154
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 768
bin: 6.75e1
variant carriers: 0

GenotypeQuality
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bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 18
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 30
bin: 9.75e1
variant carriers: 7

GenotypeQuality
all individuals: 110
bin: 7.75e1
variant carriers: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 3848
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 4620
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 2
allele frequency: 6.901311249137337e-5
allele num: 28980
num of homozygotes: 0

East Asian
type: Population
allele count: 2
allele frequency: 5.36480686695279e-4
allele num: 3728
num of homozygotes: 0

South Asian
type: Population
allele count: 3
allele frequency: 2.941176470588235e-4
allele num: 10200
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1336
num of homozygotes: 0

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

VQSLOD
type: SiteQuality
SIO_000300: 1.81e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 2.78e-1

DP
type: SiteQuality
SIO_000300: 6.88939e5

FS
type: SiteQuality
SIO_000300: 1.443e0

MQ
type: SiteQuality
SIO_000300: 5.952e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.46e-2

MQRankSum
type: SiteQuality
SIO_000300: 3.01e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 0.0e0

QD
type: SiteQuality
SIO_000300: 1.103e1

BaseQRankSum
type: SiteQuality
SIO_000300: -2.41e-1

GenotypeQuality
all individuals: 31070
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2610
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 747
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 31
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 450
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3214
bin: 1.75e1
variant carriers: 0

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

GenotypeQuality
all individuals: 108
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 456
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 341
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 19
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 8104
bin: 6.25e1
variant carriers: 1

GenotypeQuality
all individuals: 26
bin: 9.75e1
variant carriers: 4

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 3.658179689786362e-5
allele num: 27336
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10022
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1180
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 3672
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 372
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 3522
num of homozygotes: 0

Latino
type: Population
allele count: 3
allele frequency: 7.035647279549719e-4
allele num: 4264
num of homozygotes: 0

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.62e-2

ReadPosRankSum
type: SiteQuality
SIO_000300: 4.74e-1

DP
type: SiteQuality
SIO_000300: 6.70994e5

MQ
type: SiteQuality
SIO_000300: 6.0e1

VQSLOD
type: SiteQuality
SIO_000300: 1.38e0

MQRankSum
type: SiteQuality
SIO_000300: 5.78e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 6.63e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 4.37e-1

FS
type: SiteQuality
SIO_000300: 7.204e0

QD
type: SiteQuality
SIO_000300: 1.342e1

GenotypeQuality
all individuals: 1783
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2144
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 802
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variant carriers: 0

GenotypeQuality
all individuals: 12
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variant carriers: 0

GenotypeQuality
all individuals: 2085
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variant carriers: 0

GenotypeQuality
all individuals: 157
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 213
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1475
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variant carriers: 0

GenotypeQuality
all individuals: 23
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variant carriers: 1

GenotypeQuality
all individuals: 33080
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variant carriers: 0

GenotypeQuality
all individuals: 745
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 8187
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 84
bin: 5.75e1
variant carriers: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 4.200268817204301e-5
allele num: 23808
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 336
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 3366
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9610
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 3434
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 934
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 3004
num of homozygotes: 0

QD
type: SiteQuality
SIO_000300: 6.53e0

ClippingRankSum
type: SiteQuality
SIO_000300: 2.34e-1

MQRankSum
type: SiteQuality
SIO_000300: 8.95e-1

VQSLOD
type: SiteQuality
SIO_000300: -9.487e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 7.68e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 1.68e0

DP
type: SiteQuality
SIO_000300: 6.39249e5

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.91e-2

FS
type: SiteQuality
SIO_000300: 5.859e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

GenotypeQuality
all individuals: 8048
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 460
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 684
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 33446
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 167
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 8387
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GenotypeQuality
all individuals: 1636
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 24
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variant carriers: 1

GenotypeQuality
all individuals: 53
bin: 5.75e1
variant carriers: 0

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

GenotypeQuality
all individuals: 108
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1953
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 191
bin: 4.75e1
variant carriers: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9544
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 4.35691878703381e-5
allele num: 22952
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 332
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 3246
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 3278
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2868
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 918
num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: 2.25e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.69e-2

FS
type: SiteQuality
SIO_000300: 2.332e0

MQRankSum
type: SiteQuality
SIO_000300: 1.36e0

BaseQRankSum
type: SiteQuality
SIO_000300: 1.93e0

ReadPosRankSum
type: SiteQuality
SIO_000300: -5.28e-1

QD
type: SiteQuality
SIO_000300: 9.33e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

ClippingRankSum
type: SiteQuality
SIO_000300: 3.85e-1

DP
type: SiteQuality
SIO_000300: 6.27171e5

GenotypeQuality
all individuals: 1636
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 460
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 33446
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 53
bin: 5.75e1
variant carriers: 0

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

GenotypeQuality
all individuals: 167
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 18
bin: 9.25e1
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GenotypeQuality
all individuals: 30
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 24
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 186
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 762
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 108
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1953
bin: 2.75e1
variant carriers: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 918
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9544
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 3246
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 4.35691878703381e-5
allele num: 22952
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 3278
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 332
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2868
num of homozygotes: 0

MQ
type: SiteQuality
SIO_000300: 6.0e1

MQRankSum
type: SiteQuality
SIO_000300: 1.36e0

ClippingRankSum
type: SiteQuality
SIO_000300: 3.85e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: -5.28e-1

FS
type: SiteQuality
SIO_000300: 2.332e0

DP
type: SiteQuality
SIO_000300: 6.27171e5

QD
type: SiteQuality
SIO_000300: 9.33e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.69e-2

BaseQRankSum
type: SiteQuality
SIO_000300: 1.93e0

VQSLOD
type: SiteQuality
SIO_000300: 2.25e-1

GenotypeQuality
all individuals: 131
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 50
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 122
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1042
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 27
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 7273
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2342
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 11
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 11576
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 1439
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 23
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 99
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 18
bin: 9.25e1
variant carriers: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2502
num of homozygotes: 0

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

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2366
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2868
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 1.093374152635032e-4
allele num: 9146
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 18670
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 298
num of homozygotes: 0

MQRankSum
type: SiteQuality
SIO_000300: -7.88e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -3.0e-2

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.55e0

QD
type: SiteQuality
SIO_000300: 9.73e0

DP
type: SiteQuality
SIO_000300: 5.82975e5

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.63e-2

FS
type: SiteQuality
SIO_000300: 7.11e0

ClippingRankSum
type: SiteQuality
SIO_000300: 2.5e-1

MQ
type: SiteQuality
SIO_000300: 5.938e1

VQSLOD
type: SiteQuality
SIO_000300: -1.177e0

GenotypeQuality
all individuals: 1399
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 91
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 753
bin: 2.5e0
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GenotypeQuality
all individuals: 144
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 28
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variant carriers: 0

GenotypeQuality
all individuals: 119
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GenotypeQuality
all individuals: 16
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GenotypeQuality
all individuals: 6991
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 95
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 76
bin: 5.75e1
variant carriers: 1

GenotypeQuality
all individuals: 30662
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 11
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 693
bin: 6.75e1
variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2262
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 272
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9020
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 510
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2714
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 5.717552887364208e-5
allele num: 17490
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2366
num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: -7.439e-1

FS
type: SiteQuality
SIO_000300: 0.0e0

BaseQRankSum
type: SiteQuality
SIO_000300: 5.37e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 7.2e-1

MQ
type: SiteQuality
SIO_000300: 5.89e1

ClippingRankSum
type: SiteQuality
SIO_000300: 7.32e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.81e-2

QD
type: SiteQuality
SIO_000300: 1.171e1

MQRankSum
type: SiteQuality
SIO_000300: -3.42e-1

DP
type: SiteQuality
SIO_000300: 5.66478e5

GenotypeQuality
all individuals: 95
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 90
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 47
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 13177
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 109
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 728
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 28
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 16
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 11
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 23
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 1205
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 7000
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 96
bin: 5.25e1
variant carriers: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2336
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 1.114081996434938e-4
allele num: 8976
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 17232
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 276
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2234
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2690
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 496
num of homozygotes: 0

ClippingRankSum
type: SiteQuality
SIO_000300: 8.61e-1

FS
type: SiteQuality
SIO_000300: 2.01e0

MQRankSum
type: SiteQuality
SIO_000300: 3.36e-1

DP
type: SiteQuality
SIO_000300: 5.63464e5

VQSLOD
type: SiteQuality
SIO_000300: -2.904e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

InbreedingCoeff
type: SiteQuality
SIO_000300: 2.41e-2

BaseQRankSum
type: SiteQuality
SIO_000300: -6.76e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: -3.36e-1

QD
type: SiteQuality
SIO_000300: 2.31e0

GenotypeQuality
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bin: 4.25e1
variant carriers: 0

GenotypeQuality
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bin: 4.75e1
variant carriers: 0

GenotypeQuality
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bin: 3.25e1
variant carriers: 0

GenotypeQuality
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bin: 2.75e1
variant carriers: 0

GenotypeQuality
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bin: 1.25e1
variant carriers: 0

GenotypeQuality
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bin: 9.25e1
variant carriers: 0

GenotypeQuality
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bin: 2.25e1
variant carriers: 0

GenotypeQuality
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GenotypeQuality
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bin: 7.25e1
variant carriers: 0

GenotypeQuality
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bin: 3.75e1
variant carriers: 0

GenotypeQuality
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bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 12
bin: 8.75e1
variant carriers: 1

GenotypeQuality
all individuals: 27
bin: 8.25e1
variant carriers: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 448
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 1.131733816206428e-4
allele num: 8836
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2130
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2590
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2102
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16232
num of homozygotes: 0

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

MQRankSum
type: SiteQuality
SIO_000300: -7.31e-1

FS
type: SiteQuality
SIO_000300: 0.0e0

ClippingRankSum
type: SiteQuality
SIO_000300: 5.46e-1

QD
type: SiteQuality
SIO_000300: 1.164e1

DP
type: SiteQuality
SIO_000300: 5.48577e5

BaseQRankSum
type: SiteQuality
SIO_000300: -1.58e0

ReadPosRankSum
type: SiteQuality
SIO_000300: -5.46e-1

VQSLOD
type: SiteQuality
SIO_000300: -2.111e0

MQ
type: SiteQuality
SIO_000300: 5.829e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -3.06e-2

GenotypeQuality
all individuals: 1057
bin: 2.75e1
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
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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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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 15
bin: 9.25e1
variant carriers: 0

European (Non-Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 15812
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 420
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2532
num of homozygotes: 0

East Asian
type: Population
allele count: 1
allele frequency: 4.930966469428008e-4
allele num: 2028
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2072
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8760
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 252
num of homozygotes: 0

MQRankSum
type: SiteQuality
SIO_000300: -1.097e0

VQSLOD
type: SiteQuality
SIO_000300: -2.881e0

BaseQRankSum
type: SiteQuality
SIO_000300: -6.5e-2

InbreedingCoeff
type: SiteQuality
SIO_000300: -3.17e-2

DP
type: SiteQuality
SIO_000300: 5.40044e5

MQ
type: SiteQuality
SIO_000300: 6.0e1

ClippingRankSum
type: SiteQuality
SIO_000300: 1.1e0

FS
type: SiteQuality
SIO_000300: 0.0e0

ReadPosRankSum
type: SiteQuality
SIO_000300: -1.097e0

QD
type: SiteQuality
SIO_000300: 5.17e0

GenotypeQuality
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bin: 8.25e1
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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variant carriers: 0

GenotypeQuality
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bin: 3.75e1
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
all individuals: 84
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 84
bin: 5.25e1
variant carriers: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 380
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8694
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1976
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2462
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1964
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 244
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 6.541077969649399e-5
allele num: 15288
num of homozygotes: 0

MQRankSum
type: SiteQuality
SIO_000300: -1.035e0

BaseQRankSum
type: SiteQuality
SIO_000300: 3.17e0

FS
type: SiteQuality
SIO_000300: 0.0e0

VQSLOD
type: SiteQuality
SIO_000300: -1.1e0

ClippingRankSum
type: SiteQuality
SIO_000300: 1.48e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 2.8e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -3.38e-2

DP
type: SiteQuality
SIO_000300: 5.35265e5

QD
type: SiteQuality
SIO_000300: 9.77e0

GenotypeQuality
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bin: 2.5e0
variant carriers: 0

GenotypeQuality
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bin: 6.25e1
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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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
all individuals: 22
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variant carriers: 1

GenotypeQuality
all individuals: 11
bin: 8.75e1
variant carriers: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8694
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 15086
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 244
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1936
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1952
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 380
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2452
num of homozygotes: 0

MQRankSum
type: SiteQuality
SIO_000300: 7.36e-1

VQSLOD
type: SiteQuality
SIO_000300: -1.466e0

QD
type: SiteQuality
SIO_000300: 4.91e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -3.38e-2

ClippingRankSum
type: SiteQuality
SIO_000300: 7.29e-1

FS
type: SiteQuality
SIO_000300: 2.158e0

MQ
type: SiteQuality
SIO_000300: 5.652e1

BaseQRankSum
type: SiteQuality
SIO_000300: -1.307e0

DP
type: SiteQuality
SIO_000300: 5.31231e5

ReadPosRankSum
type: SiteQuality
SIO_000300: -7.36e-1

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: 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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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 15
bin: 9.25e1
variant carriers: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 12828
num of homozygotes: 0

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

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 284
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2176
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1600
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8408
num of homozygotes: 0

East Asian
type: Population
allele count: 2
allele frequency: 1.242236024844721e-3
allele num: 1610
num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: -2.124e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -4.11e-2

FS
type: SiteQuality
SIO_000300: 0.0e0

QD
type: SiteQuality
SIO_000300: 6.09e0

MQRankSum
type: SiteQuality
SIO_000300: 8.100000000000001e-1

DP
type: SiteQuality
SIO_000300: 4.92671e5

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.64e0

BaseQRankSum
type: SiteQuality
SIO_000300: -1.042e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

ClippingRankSum
type: SiteQuality
SIO_000300: 1.43e0

GenotypeQuality
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bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 20969
bin: 7.5e0
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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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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variant carriers: 0

GenotypeQuality
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bin: 5.75e1
variant carriers: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8360
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1508
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2116
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 266
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 8.111615833874107e-5
allele num: 12328
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1530
num of homozygotes: 0

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

QD
type: SiteQuality
SIO_000300: 3.87e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

MQRankSum
type: SiteQuality
SIO_000300: 8.51e-1

FS
type: SiteQuality
SIO_000300: 0.0e0

ClippingRankSum
type: SiteQuality
SIO_000300: 2.78e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 3.36e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 3.48e-2

VQSLOD
type: SiteQuality
SIO_000300: -2.434e0

BaseQRankSum
type: SiteQuality
SIO_000300: -1.034e0

DP
type: SiteQuality
SIO_000300: 4.83918e5

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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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: 5.25e1
variant carriers: 1

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 178
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1038
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 160
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7814
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1730
num of homozygotes: 0

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

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8894
num of homozygotes: 0

InbreedingCoeff
type: SiteQuality
SIO_000300: -5.75e-2

BaseQRankSum
type: SiteQuality
SIO_000300: -7.42e-1

MQRankSum
type: SiteQuality
SIO_000300: 7.42e-1

FS
type: SiteQuality
SIO_000300: 0.0e0

VQSLOD
type: SiteQuality
SIO_000300: -1.719e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 0.0e0

ClippingRankSum
type: SiteQuality
SIO_000300: 7.42e-1

DP
type: SiteQuality
SIO_000300: 4.05118e5

QD
type: SiteQuality
SIO_000300: 1.692e1

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: 22
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GenotypeQuality
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variant carriers: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 174
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1014
num of homozygotes: 0

European (Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 158
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7752
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.155001155001155e-4
allele num: 8658
num of homozygotes: 0

Latino
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: 1700
num of homozygotes: 0

MQRankSum
type: SiteQuality
SIO_000300: 1.59e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -5.87e-2

VQSLOD
type: SiteQuality
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BaseQRankSum
type: SiteQuality
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QD
type: SiteQuality
SIO_000300: 1.119e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 7.22e-1

DP
type: SiteQuality
SIO_000300: 3.97977e5

ClippingRankSum
type: SiteQuality
SIO_000300: -1.01e0

FS
type: SiteQuality
SIO_000300: 0.0e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

GenotypeQuality
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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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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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bin: 4.75e1
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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: 674
num of homozygotes: 0

East Asian
type: Population
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 (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8170
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1598
num of homozygotes: 0

European (Finnish)
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: 170
num of homozygotes: 0

MQ
type: SiteQuality
SIO_000300: 6.0e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -6.22e-2

FS
type: SiteQuality
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DP
type: SiteQuality
SIO_000300: 3.77459e5

MQRankSum
type: SiteQuality
SIO_000300: 1.77e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -1.368e0

ClippingRankSum
type: SiteQuality
SIO_000300: 5.73e-1

VQSLOD
type: SiteQuality
SIO_000300: -1.375e0

QD
type: SiteQuality
SIO_000300: 9.390000000000001e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 0.0e0

GenotypeQuality
all individuals: 39
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 20
bin: 8.25e1
variant carriers: 1

GenotypeQuality
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bin: 9.25e1
variant carriers: 0

GenotypeQuality
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bin: 9.75e1
variant carriers: 0

GenotypeQuality
all individuals: 556
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 9
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 377
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 89
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 46
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 3673
bin: 6.25e1
variant carriers: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 602
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7526
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 118
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 166
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 880
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7690
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1536
num of homozygotes: 0

MQ
type: SiteQuality
SIO_000300: 5.739e1

ClippingRankSum
type: SiteQuality
SIO_000300: 2.48e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 2.48e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -6.45e-2

FS
type: SiteQuality
SIO_000300: 0.0e0

DP
type: SiteQuality
SIO_000300: 3.61541e5

ReadPosRankSum
type: SiteQuality
SIO_000300: 2.48e-1

VQSLOD
type: SiteQuality
SIO_000300: -2.71e-1

QD
type: SiteQuality
SIO_000300: 1.529e1

MQRankSum
type: SiteQuality
SIO_000300: 5.73e-1

GenotypeQuality
all individuals: 10429
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 31297
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 306
bin: 3.75e1
variant carriers: 0

GenotypeQuality
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bin: 7.75e1
variant carriers: 0

GenotypeQuality
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bin: 6.75e1
variant carriers: 0

GenotypeQuality
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bin: 8.75e1
variant carriers: 0

GenotypeQuality
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bin: 5.25e1
variant carriers: 1

GenotypeQuality
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bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 60
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 18
bin: 8.25e1
variant carriers: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 488
num of homozygotes: 0

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

South Asian
type: Population
allele count: 1
allele frequency: 1.358695652173913e-4
allele num: 7360
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 96
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 770
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1432
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6926
num of homozygotes: 0

MQ
type: SiteQuality
SIO_000300: 6.0e1

VQSLOD
type: SiteQuality
SIO_000300: 3.6e0

MQRankSum
type: SiteQuality
SIO_000300: 2.34e-1

QD
type: SiteQuality
SIO_000300: 1.039e1

FS
type: SiteQuality
SIO_000300: 0.0e0

ClippingRankSum
type: SiteQuality
SIO_000300: 1.98e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 3.58e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -6.77e-2

DP
type: SiteQuality
SIO_000300: 3.36609e5

BaseQRankSum
type: SiteQuality
SIO_000300: 8.47e-1

GenotypeQuality
all individuals: 294
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 783
bin: 3.25e1
variant carriers: 0

GenotypeQuality
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bin: 2.75e1
variant carriers: 0

GenotypeQuality
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bin: 1.75e1
variant carriers: 0

GenotypeQuality
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bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 17
bin: 8.25e1
variant carriers: 0

GenotypeQuality
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bin: 3.75e1
variant carriers: 0

GenotypeQuality
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bin: 9.75e1
variant carriers: 0

GenotypeQuality
all individuals: 74
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 9527
bin: 2.25e1
variant carriers: 1

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

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

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 450
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6626
num of homozygotes: 0

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

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1392
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7312
num of homozygotes: 0

BaseQRankSum
type: SiteQuality
SIO_000300: 7.27e-1

MQRankSum
type: SiteQuality
SIO_000300: 7.27e-1

VQSLOD
type: SiteQuality
SIO_000300: -1.539e0

FS
type: SiteQuality
SIO_000300: 3.424e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 9.25e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 7.27e-1

QD
type: SiteQuality
SIO_000300: 1.518e1

MQ
type: SiteQuality
SIO_000300: 6.0e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -6.88e-2

DP
type: SiteQuality
SIO_000300: 3.25879e5

GenotypeQuality
all individuals: 2532
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 9764
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1579
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 13
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 345
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 31372
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 22
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 38
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 17
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 63
bin: 4.25e1
variant carriers: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1384
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 454
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 710
num of homozygotes: 0

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

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 76
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 1.366867140513942e-4
allele num: 7316
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6662
num of homozygotes: 0

QD
type: SiteQuality
SIO_000300: 7.71e0

VQSLOD
type: SiteQuality
SIO_000300: -3.915e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 2.62e0

BaseQRankSum
type: SiteQuality
SIO_000300: -2.088e0

ClippingRankSum
type: SiteQuality
SIO_000300: -2.621e0

MQ
type: SiteQuality
SIO_000300: 5.896e1

FS
type: SiteQuality
SIO_000300: 3.214e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -6.82e-2

MQRankSum
type: SiteQuality
SIO_000300: -4.0e-1

DP
type: SiteQuality
SIO_000300: 3.25464e5

GenotypeQuality
all individuals: 14
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 53
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 692
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 10
bin: 8.75e1
variant carriers: 1

GenotypeQuality
all individuals: 6494
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 150
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 200
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 17
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 46
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2233
bin: 1.75e1
variant carriers: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 288
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 1.02880658436214e-3
allele num: 972
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 460
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 38
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 4844
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 136
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6672
num of homozygotes: 0

ReadPosRankSum
type: SiteQuality
SIO_000300: 4.75e-1

FS
type: SiteQuality
SIO_000300: 0.0e0

MQRankSum
type: SiteQuality
SIO_000300: 4.06e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -7.74e-2

MQ
type: SiteQuality
SIO_000300: 6.0e1

BaseQRankSum
type: SiteQuality
SIO_000300: -1.189e0

ClippingRankSum
type: SiteQuality
SIO_000300: 7.9e-2

VQSLOD
type: SiteQuality
SIO_000300: 4.64e0

DP
type: SiteQuality
SIO_000300: 2.7243e5

QD
type: SiteQuality
SIO_000300: 1.256e1

GenotypeQuality
all individuals: 11048
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 881
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 33
bin: 7.75e1
variant carriers: 2

GenotypeQuality
all individuals: 30
bin: 9.75e1
variant carriers: 0

GenotypeQuality
all individuals: 9
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 185
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 374
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 320
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 42
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 61
bin: 5.75e1
variant carriers: 0

European (Non-Finnish)
type: Population
allele count: 2
allele frequency: 5.081300813008131e-4
allele num: 3936
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 346
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 716
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 108
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6052
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 216
num of homozygotes: 0

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

FS
type: SiteQuality
SIO_000300: 9.209e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -8.85e-2

VQSLOD
type: SiteQuality
SIO_000300: 7.77e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -5.5e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 5.5e-1

MQ
type: SiteQuality
SIO_000300: 5.521e1

MQRankSum
type: SiteQuality
SIO_000300: 9.370000000000001e-1

DP
type: SiteQuality
SIO_000300: 2.65566e5

BaseQRankSum
type: SiteQuality
SIO_000300: 0.0e0

QD
type: SiteQuality
SIO_000300: 5.79e0

GenotypeQuality
all individuals: 139
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 13
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1596
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 22
bin: 7.75e1
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GenotypeQuality
all individuals: 7689
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 15
bin: 9.25e1
variant carriers: 1

GenotypeQuality
all individuals: 132
bin: 6.25e1
variant carriers: 1

GenotypeQuality
all individuals: 55
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variant carriers: 0

GenotypeQuality
all individuals: 22
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 116
bin: 9.75e1
variant carriers: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 808
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 332
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 170
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 624
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 60
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 4988
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2632
num of homozygotes: 0

ClippingRankSum
type: SiteQuality
SIO_000300: -9.88e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -1.231e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -6.01e-2

ReadPosRankSum
type: SiteQuality
SIO_000300: 9.88e-1

DP
type: SiteQuality
SIO_000300: 2.7291e5

MQ
type: SiteQuality
SIO_000300: 6.0e1

FS
type: SiteQuality
SIO_000300: 3.979e0

VQSLOD
type: SiteQuality
SIO_000300: -1.362e0

MQRankSum
type: SiteQuality
SIO_000300: 3.58e-1

QD
type: SiteQuality
SIO_000300: 9.699999999999999e0

GenotypeQuality
all individuals: 5391
bin: 1.75e1
variant carriers: 2

GenotypeQuality
all individuals: 21285
bin: 7.5e0
variant carriers: 3

GenotypeQuality
all individuals: 10010
bin: 2.25e1
variant carriers: 4

GenotypeQuality
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bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 30
bin: 7.25e1
variant carriers: 4

GenotypeQuality
all individuals: 16
bin: 9.25e1
variant carriers: 3

GenotypeQuality
all individuals: 194
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
all individuals: 161
bin: 9.75e1
variant carriers: 45

GenotypeQuality
all individuals: 14
bin: 8.75e1
variant carriers: 2

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 4998
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 174
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 614
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 814
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 64
num of homozygotes: 0

Latino
type: Population
allele count: 1
allele frequency: 2.857142857142857e-3
allele num: 350
num of homozygotes: 0

South Asian
type: Population
allele count: 40
allele frequency: 1.5600624024961e-2
allele num: 2564
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 1.748e0

DP
type: SiteQuality
SIO_000300: 2.79532e5

InbreedingCoeff
type: SiteQuality
SIO_000300: -5.86e-2

MQ
type: SiteQuality
SIO_000300: 6.0e1

ClippingRankSum
type: SiteQuality
SIO_000300: 1.03e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 4.06e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 3.58e-1

MQRankSum
type: SiteQuality
SIO_000300: 1.43e-1

VQSLOD
type: SiteQuality
SIO_000300: 2.11e0

QD
type: SiteQuality
SIO_000300: 1.291e1

GenotypeQuality
all individuals: 14963
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2791
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 22186
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 76
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variant carriers: 0

GenotypeQuality
all individuals: 118
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variant carriers: 1

GenotypeQuality
all individuals: 32
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1727
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 492
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variant carriers: 0

GenotypeQuality
all individuals: 11
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variant carriers: 0

GenotypeQuality
all individuals: 24
bin: 7.75e1
variant carriers: 0

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

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2660
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 690
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5484
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 398
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 1
allele frequency: 4.854368932038835e-3
allele num: 206
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 60
num of homozygotes: 0

QD
type: SiteQuality
SIO_000300: 1.772e1

MQRankSum
type: SiteQuality
SIO_000300: 7.42e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -5.83e-2

MQ
type: SiteQuality
SIO_000300: 5.805e1

ReadPosRankSum
type: SiteQuality
SIO_000300: -2.59e-1

FS
type: SiteQuality
SIO_000300: 0.0e0

BaseQRankSum
type: SiteQuality
SIO_000300: -7.42e-1

VQSLOD
type: SiteQuality
SIO_000300: -1.445e0

DP
type: SiteQuality
SIO_000300: 3.0443e5

ClippingRankSum
type: SiteQuality
SIO_000300: 7.42e-1

GenotypeQuality
all individuals: 520
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 33
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 5034
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GenotypeQuality
all individuals: 21444
bin: 7.5e0
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GenotypeQuality
all individuals: 128
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variant carriers: 0

GenotypeQuality
all individuals: 4683
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variant carriers: 0

GenotypeQuality
all individuals: 33
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 11
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variant carriers: 0

GenotypeQuality
all individuals: 54
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 22
bin: 8.25e1
variant carriers: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 940
num of homozygotes: 0

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

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2620
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 720
num of homozygotes: 0

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

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 60
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5836
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 0.0e0

VQSLOD
type: SiteQuality
SIO_000300: 2.91e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

MQRankSum
type: SiteQuality
SIO_000300: 1.98e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -9.22e-1

DP
type: SiteQuality
SIO_000300: 3.11746e5

QD
type: SiteQuality
SIO_000300: 1.412e1

BaseQRankSum
type: SiteQuality
SIO_000300: 1.98e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -5.93e-2

ReadPosRankSum
type: SiteQuality
SIO_000300: 9.22e-1

GenotypeQuality
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bin: 2.75e1
variant carriers: 0

GenotypeQuality
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bin: 5.25e1
variant carriers: 0

GenotypeQuality
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bin: 4.25e1
variant carriers: 0

GenotypeQuality
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bin: 1.25e1
variant carriers: 0

GenotypeQuality
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bin: 2.5e0
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GenotypeQuality
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bin: 6.25e1
variant carriers: 0

GenotypeQuality
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bin: 8.75e1
variant carriers: 0

GenotypeQuality
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bin: 8.25e1
variant carriers: 0

GenotypeQuality
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bin: 5.75e1
variant carriers: 0

GenotypeQuality
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bin: 9.75e1
variant carriers: 1

East Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 828
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1010
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 470
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2798
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 236
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 64
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6384
num of homozygotes: 0

MQRankSum
type: SiteQuality
SIO_000300: -8.98e-1

QD
type: SiteQuality
SIO_000300: 1.26e1

InbreedingCoeff
type: SiteQuality
SIO_000300: 4.81e-2

MQ
type: SiteQuality
SIO_000300: 6.0e1

VQSLOD
type: SiteQuality
SIO_000300: -2.015e0

FS
type: SiteQuality
SIO_000300: 0.0e0

BaseQRankSum
type: SiteQuality
SIO_000300: -3.61e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: -1.271e0

ClippingRankSum
type: SiteQuality
SIO_000300: 1.31e0

DP
type: SiteQuality
SIO_000300: 3.18626e5

GenotypeQuality
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bin: 2.75e1
variant carriers: 0

GenotypeQuality
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bin: 2.25e1
variant carriers: 0

GenotypeQuality
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bin: 5.75e1
variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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bin: 2.5e0
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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
variant carriers: 0

GenotypeQuality
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bin: 1.75e1
variant carriers: 0

East Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 828
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 236
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 64
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2798
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1010
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6384
num of homozygotes: 0

Latino
type: Population
allele count: 1
allele frequency: 2.127659574468085e-3
allele num: 470
num of homozygotes: 0

MQ
type: SiteQuality
SIO_000300: 6.0e1

FS
type: SiteQuality
SIO_000300: 0.0e0

ReadPosRankSum
type: SiteQuality
SIO_000300: -1.271e0

DP
type: SiteQuality
SIO_000300: 3.18626e5

VQSLOD
type: SiteQuality
SIO_000300: -2.015e0

MQRankSum
type: SiteQuality
SIO_000300: -8.98e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 4.81e-2

BaseQRankSum
type: SiteQuality
SIO_000300: -3.61e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 1.31e0

QD
type: SiteQuality
SIO_000300: 1.26e1

GenotypeQuality
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bin: 5.75e1
variant carriers: 0

GenotypeQuality
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bin: 1.25e1
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: 0

GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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bin: 2.25e1
variant carriers: 0

East Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 868
num of homozygotes: 0

European (Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 246
num of homozygotes: 0

Latino
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allele count: 0
allele frequency: 0.0e0
allele num: 482
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2576
num of homozygotes: 0

African
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allele count: 0
allele frequency: 0.0e0
allele num: 1008
num of homozygotes: 0

European (Non-Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 6494
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 70
num of homozygotes: 0

ClippingRankSum
type: SiteQuality
SIO_000300: 1.18e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -5.99e-2

FS
type: SiteQuality
SIO_000300: 1.1073e1

VQSLOD
type: SiteQuality
SIO_000300: -7.466e-1

MQ
type: SiteQuality
SIO_000300: 5.871e1

BaseQRankSum
type: SiteQuality
SIO_000300: -1.032e0

MQRankSum
type: SiteQuality
SIO_000300: -8.73e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: -8.500000000000001e-2

QD
type: SiteQuality
SIO_000300: 2.471e1

DP
type: SiteQuality
SIO_000300: 3.44269e5

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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bin: 3.25e1
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
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variant carriers: 2

GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 44
bin: 8.25e1
variant carriers: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 15734
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2074
num of homozygotes: 0

East Asian
type: Population
allele count: 1
allele frequency: 4.892367906066536e-4
allele num: 2044
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 804
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5022
num of homozygotes: 0

Latino
type: Population
allele count: 1
allele frequency: 5.208333333333333e-4
allele num: 1920
num of homozygotes: 0

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

MQRankSum
type: SiteQuality
SIO_000300: 1.98e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -2.329e0

DP
type: SiteQuality
SIO_000300: 5.00681e5

FS
type: SiteQuality
SIO_000300: 3.522e0

ClippingRankSum
type: SiteQuality
SIO_000300: -5.55e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.98e-1

QD
type: SiteQuality
SIO_000300: 1.116e1

MQ
type: SiteQuality
SIO_000300: 6.0e1

VQSLOD
type: SiteQuality
SIO_000300: 5.87e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.92e-2

GenotypeQuality
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bin: 2.25e1
variant carriers: 0

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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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
all individuals: 45
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variant carriers: 1

GenotypeQuality
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bin: 6.75e1
variant carriers: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 15436
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 148
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 4508
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 814
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 4.901960784313725e-4
allele num: 2040
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1808
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2012
num of homozygotes: 0

QD
type: SiteQuality
SIO_000300: 1.235e1

FS
type: SiteQuality
SIO_000300: 6.168e0

VQSLOD
type: SiteQuality
SIO_000300: 1.54e-1

DP
type: SiteQuality
SIO_000300: 5.24764e5

ReadPosRankSum
type: SiteQuality
SIO_000300: 0.0e0

MQRankSum
type: SiteQuality
SIO_000300: 3.49e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 3.04e-2

BaseQRankSum
type: SiteQuality
SIO_000300: 4.0e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

ClippingRankSum
type: SiteQuality
SIO_000300: 5.5e-1

GenotypeQuality
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bin: 2.5e0
variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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bin: 6.25e1
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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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 123
bin: 9.75e1
variant carriers: 2

European (Non-Finnish)
type: Population
allele count: 2
allele frequency: 1.295672454003628e-4
allele num: 15436
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1808
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2012
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2040
num of homozygotes: 0

European (Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 814
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 4508
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 148
num of homozygotes: 0

QD
type: SiteQuality
SIO_000300: 1.235e1

FS
type: SiteQuality
SIO_000300: 6.168e0

VQSLOD
type: SiteQuality
SIO_000300: 1.54e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

InbreedingCoeff
type: SiteQuality
SIO_000300: 3.04e-2

ReadPosRankSum
type: SiteQuality
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MQRankSum
type: SiteQuality
SIO_000300: 3.49e-1

DP
type: SiteQuality
SIO_000300: 5.24764e5

BaseQRankSum
type: SiteQuality
SIO_000300: 4.0e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 5.5e-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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variant carriers: 1

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: 2512
num of homozygotes: 0

Other
type: Population
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allele frequency: 0.0e0
allele num: 198
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African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2500
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European (Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 1088
num of homozygotes: 0

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

European (Non-Finnish)
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allele count: 1
allele frequency: 5.102561485865905e-5
allele num: 19598
num of homozygotes: 0

South Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 5930
num of homozygotes: 0

MQRankSum
type: SiteQuality
SIO_000300: -1.13e-1

VQSLOD
type: SiteQuality
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ReadPosRankSum
type: SiteQuality
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DP
type: SiteQuality
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InbreedingCoeff
type: SiteQuality
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BaseQRankSum
type: SiteQuality
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FS
type: SiteQuality
SIO_000300: 6.96e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

ClippingRankSum
type: SiteQuality
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QD
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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variant carriers: 2

East Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 2796
num of homozygotes: 0

European (Non-Finnish)
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allele frequency: 0.0e0
allele num: 21726
num of homozygotes: 0

African
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allele frequency: 7.326007326007326e-4
allele num: 2730
num of homozygotes: 0

Latino
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allele frequency: 0.0e0
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num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 214
num of homozygotes: 0

European (Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 1206
num of homozygotes: 0

South Asian
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allele frequency: 0.0e0
allele num: 6272
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 3.378e0

ClippingRankSum
type: SiteQuality
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BaseQRankSum
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MQ
type: SiteQuality
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ReadPosRankSum
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QD
type: SiteQuality
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MQRankSum
type: SiteQuality
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InbreedingCoeff
type: SiteQuality
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VQSLOD
type: SiteQuality
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DP
type: SiteQuality
SIO_000300: 5.88167e5

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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bin: 3.25e1
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GenotypeQuality
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variant carriers: 0

East Asian
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allele frequency: 0.0e0
allele num: 3140
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6706
num of homozygotes: 0

African
type: Population
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allele frequency: 3.205128205128205e-4
allele num: 3120
num of homozygotes: 0

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

European (Non-Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 24614
num of homozygotes: 0

European (Finnish)
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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: 246
num of homozygotes: 0

InbreedingCoeff
type: SiteQuality
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ClippingRankSum
type: SiteQuality
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MQ
type: SiteQuality
SIO_000300: 5.54e1

MQRankSum
type: SiteQuality
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VQSLOD
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ReadPosRankSum
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FS
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QD
type: SiteQuality
SIO_000300: 1.068e1

DP
type: SiteQuality
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BaseQRankSum
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GenotypeQuality
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bin: 3.25e1
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
all individuals: 220
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GenotypeQuality
all individuals: 324
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variant carriers: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 336
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7736
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 1920
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 30706
num of homozygotes: 0

Latino
type: Population
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: 3940
num of homozygotes: 0

African
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allele count: 1
allele frequency: 2.613695765812859e-4
allele num: 3826
num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: -2.022e0

BaseQRankSum
type: SiteQuality
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ReadPosRankSum
type: SiteQuality
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QD
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DP
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MQRankSum
type: SiteQuality
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FS
type: SiteQuality
SIO_000300: 3.68e0

ClippingRankSum
type: SiteQuality
SIO_000300: 2.25e-1

MQ
type: SiteQuality
SIO_000300: 5.833e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.48e-2

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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bin: 7.25e1
variant carriers: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 2108
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5226
num of homozygotes: 0

South Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 8262
num of homozygotes: 0

African
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allele count: 0
allele frequency: 0.0e0
allele num: 4144
num of homozygotes: 0

European (Non-Finnish)
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allele count: 1
allele frequency: 3.006433768264085e-5
allele num: 33262
num of homozygotes: 0

East Asian
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allele count: 0
allele frequency: 0.0e0
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Other
type: Population
allele count: 0
allele frequency: 0.0e0
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VQSLOD
type: SiteQuality
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InbreedingCoeff
type: SiteQuality
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QD
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ClippingRankSum
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SIO_000300: 1.81e0

MQRankSum
type: SiteQuality
SIO_000300: 2.39e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 9.25e-1

DP
type: SiteQuality
SIO_000300: 7.87192e5

MQ
type: SiteQuality
SIO_000300: 6.0e1

FS
type: SiteQuality
SIO_000300: 0.0e0

BaseQRankSum
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SIO_000300: -1.536e0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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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
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allele frequency: 0.0e0
allele num: 5408
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 42020
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 486
num of homozygotes: 0

European (Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 3074
num of homozygotes: 0

South Asian
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allele count: 1
allele frequency: 9.68429207824908e-5
allele num: 10326
num of homozygotes: 0

Latino
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allele count: 0
allele frequency: 0.0e0
allele num: 7628
num of homozygotes: 0

East Asian
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allele frequency: 0.0e0
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MQRankSum
type: SiteQuality
SIO_000300: 0.0e0

DP
type: SiteQuality
SIO_000300: 9.55563e5

VQSLOD
type: SiteQuality
SIO_000300: 6.899999999999999e-1

MQ
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QD
type: SiteQuality
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InbreedingCoeff
type: SiteQuality
SIO_000300: -1.0e-2

BaseQRankSum
type: SiteQuality
SIO_000300: -3.53e-1

FS
type: SiteQuality
SIO_000300: 0.0e0

ClippingRankSum
type: SiteQuality
SIO_000300: -1.678e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.33e0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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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: 2

European (Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 3858
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 8.257638315441784e-5
allele num: 12110
num of homozygotes: 0

African
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allele count: 0
allele frequency: 0.0e0
allele num: 6240
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9258
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6760
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 604
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 2.085592725452574e-5
allele num: 47948
num of homozygotes: 0

InbreedingCoeff
type: SiteQuality
SIO_000300: -7.3e-3

ReadPosRankSum
type: SiteQuality
SIO_000300: 5.78e-1

FS
type: SiteQuality
SIO_000300: 4.567e0

QD
type: SiteQuality
SIO_000300: 1.88e1

VQSLOD
type: SiteQuality
SIO_000300: -6.522e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -2.689e0

ClippingRankSum
type: SiteQuality
SIO_000300: -4.19e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

MQRankSum
type: SiteQuality
SIO_000300: -4.69e-1

DP
type: SiteQuality
SIO_000300: 1.076083e6

GenotypeQuality
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bin: 7.25e1
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
all individuals: 472
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variant carriers: 0

Latino
type: Population
allele count: 1
allele frequency: 1.040582726326743e-4
allele num: 9610
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 630
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7022
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 12606
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 4078
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6444
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 49590
num of homozygotes: 0

InbreedingCoeff
type: SiteQuality
SIO_000300: -6.6e-3

MQ
type: SiteQuality
SIO_000300: 5.863e1

FS
type: SiteQuality
SIO_000300: 0.0e0

ClippingRankSum
type: SiteQuality
SIO_000300: -9.57e-1

MQRankSum
type: SiteQuality
SIO_000300: -3.19e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 6.73e-1

QD
type: SiteQuality
SIO_000300: 1.056e1

BaseQRankSum
type: SiteQuality
SIO_000300: -3.19e-1

VQSLOD
type: SiteQuality
SIO_000300: -9.78e-1

DP
type: SiteQuality
SIO_000300: 1.109293e6

GenotypeQuality
all individuals: 10127
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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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variant carriers: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 654
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 4434
num of homozygotes: 0

European (Non-Finnish)
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allele count: 1
allele frequency: 1.93475989629687e-5
allele num: 51686
num of homozygotes: 0

South Asian
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allele count: 0
allele frequency: 0.0e0
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East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7390
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African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6746
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Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10048
num of homozygotes: 0

DP
type: SiteQuality
SIO_000300: 1.155212e6

MQ
type: SiteQuality
SIO_000300: 5.911e1

FS
type: SiteQuality
SIO_000300: 0.0e0

MQRankSum
type: SiteQuality
SIO_000300: 1.62e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 1.62e-1

VQSLOD
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SIO_000300: -1.015e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -5.5e-3

BaseQRankSum
type: SiteQuality
SIO_000300: -2.803e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 5.4e-2

QD
type: SiteQuality
SIO_000300: 6.23e0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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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
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allele count: 0
allele frequency: 0.0e0
allele num: 7248
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 54612
num of homozygotes: 0

South Asian
type: Population
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allele frequency: 7.011639321273313e-5
allele num: 14262
num of homozygotes: 0

East Asian
type: Population
allele count: 10
allele frequency: 1.287001287001287e-3
allele num: 7770
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 702
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Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10606
num of homozygotes: 0

European (Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 4980
num of homozygotes: 0

InbreedingCoeff
type: SiteQuality
SIO_000300: -3.9e-3

BaseQRankSum
type: SiteQuality
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MQRankSum
type: SiteQuality
SIO_000300: 8.57e-1

ReadPosRankSum
type: SiteQuality
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FS
type: SiteQuality
SIO_000300: 1.668e0

DP
type: SiteQuality
SIO_000300: 1.220635e6

VQSLOD
type: SiteQuality
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MQ
type: SiteQuality
SIO_000300: 5.957e1

ClippingRankSum
type: SiteQuality
SIO_000300: 3.54e-1

QD
type: SiteQuality
SIO_000300: 1.336e1

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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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: 4

African
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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: 724
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European (Non-Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 55384
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East Asian
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South Asian
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Latino
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allele count: 4
allele frequency: 3.716090672612412e-4
allele num: 10764
num of homozygotes: 0

European (Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 5156
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ClippingRankSum
type: SiteQuality
SIO_000300: -8.6e-1

MQ
type: SiteQuality
SIO_000300: 5.938e1

MQRankSum
type: SiteQuality
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ReadPosRankSum
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VQSLOD
type: SiteQuality
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InbreedingCoeff
type: SiteQuality
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FS
type: SiteQuality
SIO_000300: 1.994e0

BaseQRankSum
type: SiteQuality
SIO_000300: 2.09e-1

DP
type: SiteQuality
SIO_000300: 1.240595e6

QD
type: SiteQuality
SIO_000300: 1.586e1

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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East Asian
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allele count: 0
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num of homozygotes: 0

Other
type: Population
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allele frequency: 0.0e0
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European (Non-Finnish)
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allele count: 1
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allele num: 55384
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Latino
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African
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South Asian
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European (Finnish)
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allele frequency: 0.0e0
allele num: 5156
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MQ
type: SiteQuality
SIO_000300: 5.938e1

DP
type: SiteQuality
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MQRankSum
type: SiteQuality
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ClippingRankSum
type: SiteQuality
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InbreedingCoeff
type: SiteQuality
SIO_000300: 8.6e-3

VQSLOD
type: SiteQuality
SIO_000300: 8.179999999999999e-1

FS
type: SiteQuality
SIO_000300: 1.994e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 4.06e-1

QD
type: SiteQuality
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BaseQRankSum
type: SiteQuality
SIO_000300: 2.09e-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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East Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 8002
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European (Finnish)
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allele frequency: 0.0e0
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South Asian
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allele num: 15026
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African
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allele frequency: 0.0e0
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Latino
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allele frequency: 0.0e0
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European (Non-Finnish)
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allele count: 0
allele frequency: 0.0e0
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Other
type: Population
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MQ
type: SiteQuality
SIO_000300: 5.976e1

QD
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FS
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InbreedingCoeff
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VQSLOD
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MQRankSum
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ClippingRankSum
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DP
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SIO_000300: 1.26792e6

BaseQRankSum
type: SiteQuality
SIO_000300: -2.231e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.59e0

GenotypeQuality
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bin: 2.25e1
variant carriers: 0

GenotypeQuality
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bin: 2.75e1
variant carriers: 0

GenotypeQuality
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bin: 7.75e1
variant carriers: 0

GenotypeQuality
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bin: 1.25e1
variant carriers: 0

GenotypeQuality
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bin: 3.75e1
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GenotypeQuality
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bin: 1.75e1
variant carriers: 0

GenotypeQuality
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bin: 7.25e1
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GenotypeQuality
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bin: 8.75e1
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GenotypeQuality
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bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 313
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 441
bin: 3.25e1
variant carriers: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11094
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5856
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7992
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 15734
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8170
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 786
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 58502
num of homozygotes: 0

MQ
type: SiteQuality
SIO_000300: 6.0e1

DP
type: SiteQuality
SIO_000300: 1.315098e6

ClippingRankSum
type: SiteQuality
SIO_000300: -3.3e-2

InbreedingCoeff
type: SiteQuality
SIO_000300: 8.0e-4

FS
type: SiteQuality
SIO_000300: 0.0e0

QD
type: SiteQuality
SIO_000300: 1.02e1

VQSLOD
type: SiteQuality
SIO_000300: 6.64e-1

MQRankSum
type: SiteQuality
SIO_000300: 6.31e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -5.55e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 0.0e0

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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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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variant carriers: 0

South Asian
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allele count: 1
allele frequency: 6.338742393509128e-5
allele num: 15776
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 784
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8178
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 58598
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5898
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8006
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11104
num of homozygotes: 0

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.2e-3

VQSLOD
type: SiteQuality
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MQRankSum
type: SiteQuality
SIO_000300: -4.0e-2

FS
type: SiteQuality
SIO_000300: 3.087e0

MQ
type: SiteQuality
SIO_000300: 6.054e1

DP
type: SiteQuality
SIO_000300: 1.318916e6

ClippingRankSum
type: SiteQuality
SIO_000300: -1.796e0

QD
type: SiteQuality
SIO_000300: 1.329e1

BaseQRankSum
type: SiteQuality
SIO_000300: 1.16e0

ReadPosRankSum
type: SiteQuality
SIO_000300: -1.2e-1

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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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: 8214
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 6.255473539346929e-5
allele num: 15986
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8256
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11194
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 806
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 59684
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6154
num of homozygotes: 0

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.4e-2

QD
type: SiteQuality
SIO_000300: 1.19e1

VQSLOD
type: SiteQuality
SIO_000300: 5.05e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 8.3e-3

FS
type: SiteQuality
SIO_000300: 0.0e0

ClippingRankSum
type: SiteQuality
SIO_000300: -9.08e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 5.99e-1

DP
type: SiteQuality
SIO_000300: 1.353433e6

MQRankSum
type: SiteQuality
SIO_000300: 3.44e-1

MQ
type: SiteQuality
SIO_000300: 6.079e1

GenotypeQuality
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bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 229
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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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variant carriers: 8

GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 287
bin: 5.25e1
variant carriers: 0

South Asian
type: Population
allele count: 1
allele frequency: 6.255473539346929e-5
allele num: 15986
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8214
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6154
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11194
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 806
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8256
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 7
allele frequency: 1.172843643187454e-4
allele num: 59684
num of homozygotes: 0

MQRankSum
type: SiteQuality
SIO_000300: 3.44e-1

VQSLOD
type: SiteQuality
SIO_000300: 5.05e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.4e-2

MQ
type: SiteQuality
SIO_000300: 6.079e1

BaseQRankSum
type: SiteQuality
SIO_000300: 5.99e-1

DP
type: SiteQuality
SIO_000300: 1.353433e6

FS
type: SiteQuality
SIO_000300: 0.0e0

ClippingRankSum
type: SiteQuality
SIO_000300: -9.08e-1

QD
type: SiteQuality
SIO_000300: 1.19e1

InbreedingCoeff
type: SiteQuality
SIO_000300: 8.3e-3

GenotypeQuality
all individuals: 297
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 286
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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
all individuals: 2081
bin: 7.25e1
variant carriers: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11228
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8270
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 814
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6192
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8252
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.670732114812711e-5
allele num: 59854
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16026
num of homozygotes: 0

ClippingRankSum
type: SiteQuality
SIO_000300: -2.51e-1

FS
type: SiteQuality
SIO_000300: 0.0e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

InbreedingCoeff
type: SiteQuality
SIO_000300: 2.0e-4

QD
type: SiteQuality
SIO_000300: 2.909e1

MQRankSum
type: SiteQuality
SIO_000300: 3.71e-1

VQSLOD
type: SiteQuality
SIO_000300: -3.403e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 2.13e0

BaseQRankSum
type: SiteQuality
SIO_000300: -2.757e0

DP
type: SiteQuality
SIO_000300: 1.356357e6

GenotypeQuality
all individuals: 189
bin: 2.75e1
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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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
all individuals: 79
bin: 5.75e1
variant carriers: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 61084
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6386
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8350
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 822
num of homozygotes: 0

Latino
type: Population
allele count: 1
allele frequency: 8.841732979664014e-5
allele num: 11310
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8450
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16278
num of homozygotes: 0

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.0e-4

FS
type: SiteQuality
SIO_000300: 2.045e0

QD
type: SiteQuality
SIO_000300: 1.487e1

BaseQRankSum
type: SiteQuality
SIO_000300: -9.59e-1

DP
type: SiteQuality
SIO_000300: 1.37723e6

VQSLOD
type: SiteQuality
SIO_000300: 5.85e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 2.59e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

MQRankSum
type: SiteQuality
SIO_000300: -8.169999999999999e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -6.75e-1

GenotypeQuality
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bin: 2.25e1
variant carriers: 1

GenotypeQuality
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bin: 6.25e1
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GenotypeQuality
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variant carriers: 271

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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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

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 846
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 239
allele frequency: 3.853347091448472e-3
allele num: 62024
num of homozygotes: 1

African
type: Population
allele count: 4
allele frequency: 4.611482591653217e-4
allele num: 8674
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8418
num of homozygotes: 0

Latino
type: Population
allele count: 14
allele frequency: 1.232177433550431e-3
allele num: 11362
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 14
allele frequency: 2.14987714987715e-3
allele num: 6512
num of homozygotes: 0

South Asian
type: Population
allele count: 2
allele frequency: 1.223540927444023e-4
allele num: 16346
num of homozygotes: 0

ReadPosRankSum
type: SiteQuality
SIO_000300: 3.71e-1

VQSLOD
type: SiteQuality
SIO_000300: 5.4e0

FS
type: SiteQuality
SIO_000300: 0.0e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 6.7e-3

MQ
type: SiteQuality
SIO_000300: 5.969e1

BaseQRankSum
type: SiteQuality
SIO_000300: -4.103e0

ClippingRankSum
type: SiteQuality
SIO_000300: -9.9e-2

MQRankSum
type: SiteQuality
SIO_000300: 1.27e-1

QD
type: SiteQuality
SIO_000300: 1.278e1

DP
type: SiteQuality
SIO_000300: 1.406555e6

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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variant carriers: 0

GenotypeQuality
all individuals: 350
bin: 9.25e1
variant carriers: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16346
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8418
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 846
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 2
allele frequency: 3.071253071253071e-4
allele num: 6512
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 62024
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11362
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8674
num of homozygotes: 0

MQRankSum
type: SiteQuality
SIO_000300: 1.27e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 3.71e-1

QD
type: SiteQuality
SIO_000300: 1.278e1

ClippingRankSum
type: SiteQuality
SIO_000300: -9.9e-2

InbreedingCoeff
type: SiteQuality
SIO_000300: 6.7e-3

VQSLOD
type: SiteQuality
SIO_000300: 5.4e0

MQ
type: SiteQuality
SIO_000300: 5.969e1

DP
type: SiteQuality
SIO_000300: 1.406555e6

FS
type: SiteQuality
SIO_000300: 0.0e0

BaseQRankSum
type: SiteQuality
SIO_000300: -4.103e0

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
all individuals: 135
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variant carriers: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16364
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6540
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8434
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.604415351046079e-5
allele num: 62328
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11372
num of homozygotes: 0

African
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: 848
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VQSLOD
type: SiteQuality
SIO_000300: -1.441e0

BaseQRankSum
type: SiteQuality
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QD
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InbreedingCoeff
type: SiteQuality
SIO_000300: -1.8e-3

MQRankSum
type: SiteQuality
SIO_000300: 2.63e-1

FS
type: SiteQuality
SIO_000300: 0.0e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 2.04e0

ClippingRankSum
type: SiteQuality
SIO_000300: -1.437e0

DP
type: SiteQuality
SIO_000300: 1.402931e6

MQ
type: SiteQuality
SIO_000300: 6.0e1

GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 101
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GenotypeQuality
all individuals: 71
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GenotypeQuality
all individuals: 117
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
all individuals: 431
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GenotypeQuality
all individuals: 42821
bin: 6.25e1
variant carriers: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16366
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8438
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6548
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.598005688900252e-5
allele num: 62578
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8826
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 854
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11390
num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: -7.292e-1

QD
type: SiteQuality
SIO_000300: 3.53e0

MQRankSum
type: SiteQuality
SIO_000300: -7.232e0

ClippingRankSum
type: SiteQuality
SIO_000300: -4.04e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -8.0e-4

ReadPosRankSum
type: SiteQuality
SIO_000300: -1.913e0

MQ
type: SiteQuality
SIO_000300: 5.221e1

BaseQRankSum
type: SiteQuality
SIO_000300: 3.16e0

FS
type: SiteQuality
SIO_000300: 1.53e0

DP
type: SiteQuality
SIO_000300: 1.413117e6

GenotypeQuality
all individuals: 67
bin: 1.75e1
variant carriers: 0

GenotypeQuality
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bin: 3.75e1
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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bin: 4.75e1
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GenotypeQuality
all individuals: 1902
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GenotypeQuality
all individuals: 466
bin: 9.75e1
variant carriers: 1

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6572
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 62794
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11400
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8878
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16380
num of homozygotes: 0

East Asian
type: Population
allele count: 1
allele frequency: 1.183992422448496e-4
allele num: 8446
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 858
num of homozygotes: 0

BaseQRankSum
type: SiteQuality
SIO_000300: -2.51e0

ClippingRankSum
type: SiteQuality
SIO_000300: -2.28e-1

FS
type: SiteQuality
SIO_000300: 8.090000000000001e-1

DP
type: SiteQuality
SIO_000300: 1.413016e6

InbreedingCoeff
type: SiteQuality
SIO_000300: 3.0e-4

ReadPosRankSum
type: SiteQuality
SIO_000300: 4.6e-2

QD
type: SiteQuality
SIO_000300: 3.184e1

VQSLOD
type: SiteQuality
SIO_000300: -3.213e0

MQ
type: SiteQuality
SIO_000300: 5.922e1

MQRankSum
type: SiteQuality
SIO_000300: 1.12e0

GenotypeQuality
all individuals: 53
bin: 3.75e1
variant carriers: 0

GenotypeQuality
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bin: 2.5e0
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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
all individuals: 7699
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variant carriers: 0

GenotypeQuality
all individuals: 1245
bin: 2.25e1
variant carriers: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6590
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.581978105423021e-5
allele num: 63212
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16386
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 860
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8458
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8982
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11408
num of homozygotes: 0

ReadPosRankSum
type: SiteQuality
SIO_000300: 3.05e0

VQSLOD
type: SiteQuality
SIO_000300: -1.398e0

MQRankSum
type: SiteQuality
SIO_000300: 1.7e0

DP
type: SiteQuality
SIO_000300: 1.420022e6

QD
type: SiteQuality
SIO_000300: 1.585e1

FS
type: SiteQuality
SIO_000300: 1.884e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 5.999999999999999e-4

ClippingRankSum
type: SiteQuality
SIO_000300: -4.24e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 3.23e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

GenotypeQuality
all individuals: 522
bin: 9.75e1
variant carriers: 49

GenotypeQuality
all individuals: 614
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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: 0

GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
all individuals: 10
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variant carriers: 0

GenotypeQuality
all individuals: 7
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variant carriers: 0

GenotypeQuality
all individuals: 7743
bin: 6.75e1
variant carriers: 1

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8476
num of homozygotes: 0

Latino
type: Population
allele count: 4
allele frequency: 3.500175008750437e-4
allele num: 11428
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16394
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6608
num of homozygotes: 0

African
type: Population
allele count: 46
allele frequency: 5.04828797190518e-3
allele num: 9112
num of homozygotes: 1

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 860
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 2
allele frequency: 3.139224611520955e-5
allele num: 63710
num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: 2.81e0

BaseQRankSum
type: SiteQuality
SIO_000300: -1.321e0

FS
type: SiteQuality
SIO_000300: 7.6e-1

MQRankSum
type: SiteQuality
SIO_000300: 2.5e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -8.71e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 6.3e-3

ReadPosRankSum
type: SiteQuality
SIO_000300: 9.85e-1

DP
type: SiteQuality
SIO_000300: 1.432903e6

MQ
type: SiteQuality
SIO_000300: 5.963e1

QD
type: SiteQuality
SIO_000300: 1.567e1

GenotypeQuality
all individuals: 16
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 417
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
all individuals: 15
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 39

GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 1051
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GenotypeQuality
all individuals: 6
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variant carriers: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 860
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16396
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 38
allele frequency: 5.921954868470266e-4
allele num: 64168
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11442
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 1.08084738434933e-4
allele num: 9252
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8492
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6610
num of homozygotes: 0

DP
type: SiteQuality
SIO_000300: 1.443454e6

ClippingRankSum
type: SiteQuality
SIO_000300: -1.13e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -3.949e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 6.27e-1

MQ
type: SiteQuality
SIO_000300: 5.93e1

FS
type: SiteQuality
SIO_000300: 7.4e-1

MQRankSum
type: SiteQuality
SIO_000300: 5.46e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 3.0e-3

QD
type: SiteQuality
SIO_000300: 1.147e1

VQSLOD
type: SiteQuality
SIO_000300: 1.91e0

GenotypeQuality
all individuals: 15
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2218
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variant carriers: 0

GenotypeQuality
all individuals: 417
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variant carriers: 0

GenotypeQuality
all individuals: 16
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variant carriers: 0

GenotypeQuality
all individuals: 1913
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GenotypeQuality
all individuals: 1067
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variant carriers: 0

GenotypeQuality
all individuals: 11
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GenotypeQuality
all individuals: 374
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GenotypeQuality
all individuals: 28
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GenotypeQuality
all individuals: 1047
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GenotypeQuality
all individuals: 557
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variant carriers: 1

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8492
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11442
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 64178
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9254
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 860
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6610
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 6.099048548426445e-5
allele num: 16396
num of homozygotes: 0

ReadPosRankSum
type: SiteQuality
SIO_000300: 9.320000000000001e-1

VQSLOD
type: SiteQuality
SIO_000300: -1.392e0

FS
type: SiteQuality
SIO_000300: 4.361e0

QD
type: SiteQuality
SIO_000300: 8.67e0

MQ
type: SiteQuality
SIO_000300: 5.904e1

MQRankSum
type: SiteQuality
SIO_000300: 1.89e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -8.0e-4

DP
type: SiteQuality
SIO_000300: 1.443758e6

ClippingRankSum
type: SiteQuality
SIO_000300: -4.26e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 1.79e0

GenotypeQuality
all individuals: 484
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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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bin: 6.25e1
variant carriers: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9268
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 64238
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11442
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 862
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6610
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16400
num of homozygotes: 0

East Asian
type: Population
allele count: 1
allele frequency: 1.177301624676242e-4
allele num: 8494
num of homozygotes: 0

ReadPosRankSum
type: SiteQuality
SIO_000300: -4.78e-1

DP
type: SiteQuality
SIO_000300: 1.444616e6

MQ
type: SiteQuality
SIO_000300: 5.985e1

QD
type: SiteQuality
SIO_000300: 1.268e1

MQRankSum
type: SiteQuality
SIO_000300: 8.79e-1

VQSLOD
type: SiteQuality
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BaseQRankSum
type: SiteQuality
SIO_000300: -5.764e0

FS
type: SiteQuality
SIO_000300: 1.1201e1

ClippingRankSum
type: SiteQuality
SIO_000300: 4.71e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 2.4e-3

GenotypeQuality
all individuals: 16
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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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variant carriers: 0

African
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allele count: 0
allele frequency: 0.0e0
allele num: 9468
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 868
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6612
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11478
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16424
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8524
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.541734759951898e-5
allele num: 64862
num of homozygotes: 0

DP
type: SiteQuality
SIO_000300: 1.452958e6

BaseQRankSum
type: SiteQuality
SIO_000300: -3.644e0

FS
type: SiteQuality
SIO_000300: 3.005e0

ReadPosRankSum
type: SiteQuality
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ClippingRankSum
type: SiteQuality
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InbreedingCoeff
type: SiteQuality
SIO_000300: 7.0e-4

MQRankSum
type: SiteQuality
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QD
type: SiteQuality
SIO_000300: 7.7e-1

VQSLOD
type: SiteQuality
SIO_000300: -6.347e0

MQ
type: SiteQuality
SIO_000300: 5.939e1

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
all individuals: 1919
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variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8548
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 872
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11502
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9528
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 5
allele frequency: 7.680255598906332e-5
allele num: 65102
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16450
num of homozygotes: 0

MQ
type: SiteQuality
SIO_000300: 5.949e1

VQSLOD
type: SiteQuality
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FS
type: SiteQuality
SIO_000300: 1.149e0

DP
type: SiteQuality
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QD
type: SiteQuality
SIO_000300: 1.225e1

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.0e-4

BaseQRankSum
type: SiteQuality
SIO_000300: -1.967e0

ReadPosRankSum
type: SiteQuality
SIO_000300: -6.26e-1

MQRankSum
type: SiteQuality
SIO_000300: -4.0e-2

ClippingRankSum
type: SiteQuality
SIO_000300: 7.56e-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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bin: 4.75e1
variant carriers: 0

African
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allele count: 0
allele frequency: 0.0e0
allele num: 9536
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16448
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8548
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.535815210713847e-5
allele num: 65112
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11504
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 872
num of homozygotes: 0

DP
type: SiteQuality
SIO_000300: 1.456207e6

MQ
type: SiteQuality
SIO_000300: 5.942e1

BaseQRankSum
type: SiteQuality
SIO_000300: 6.65e-1

FS
type: SiteQuality
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VQSLOD
type: SiteQuality
SIO_000300: 6.79e-1

QD
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MQRankSum
type: SiteQuality
SIO_000300: 7.14e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 3.57e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 3.2e-3

ReadPosRankSum
type: SiteQuality
SIO_000300: -2.77e-1

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

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

GenotypeQuality
all individuals: 34
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 2224
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 20
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 9
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 42
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 565
bin: 9.75e1
variant carriers: 4

GenotypeQuality
all individuals: 1072
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1920
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 7806
bin: 6.75e1
variant carriers: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 65138
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11504
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 872
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 1.049538203190596e-4
allele num: 9528
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8548
num of homozygotes: 0

South Asian
type: Population
allele count: 3
allele frequency: 1.82370820668693e-4
allele num: 16450
num of homozygotes: 0

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.62e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 6.01e-1

VQSLOD
type: SiteQuality
SIO_000300: 2.51e0

FS
type: SiteQuality
SIO_000300: 0.0e0

DP
type: SiteQuality
SIO_000300: 1.456592e6

MQRankSum
type: SiteQuality
SIO_000300: 3.28e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 2.19e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.0e-4

QD
type: SiteQuality
SIO_000300: 1.077e1

MQ
type: SiteQuality
SIO_000300: 5.925e1

GenotypeQuality
all individuals: 375
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 19
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 64
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 575
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 419
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 20
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 487
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 30
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1073
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 25
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 7794
bin: 6.75e1
variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8550
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 872
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.534730961662421e-5
allele num: 65158
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16456
num of homozygotes: 0

African
type: Population
allele count: 28
allele frequency: 2.934395304967512e-3
allele num: 9542
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11510
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

MQRankSum
type: SiteQuality
SIO_000300: 5.6e-2

FS
type: SiteQuality
SIO_000300: 5.28e-1

QD
type: SiteQuality
SIO_000300: 1.194e1

VQSLOD
type: SiteQuality
SIO_000300: 3.37e0

ClippingRankSum
type: SiteQuality
SIO_000300: -1.35e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.0e-4

DP
type: SiteQuality
SIO_000300: 1.460865e6

BaseQRankSum
type: SiteQuality
SIO_000300: -2.367e0

MQ
type: SiteQuality
SIO_000300: 5.953e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 4.28e-1

GenotypeQuality
all individuals: 48
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 25
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 24
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 376
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 488
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 1918
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1074
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 421
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 2221
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 7799
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 64
bin: 3.25e1
variant carriers: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 872
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11510
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 3
allele frequency: 4.60433421327276e-5
allele num: 65156
num of homozygotes: 1

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16456
num of homozygotes: 0

African
type: Population
allele count: 3
allele frequency: 3.145973154362416e-4
allele num: 9536
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8550
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 2.465e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.22e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 5.8e-3

VQSLOD
type: SiteQuality
SIO_000300: 5.43e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -1.86e-1

MQRankSum
type: SiteQuality
SIO_000300: 1.22e0

DP
type: SiteQuality
SIO_000300: 1.457686e6

MQ
type: SiteQuality
SIO_000300: 5.975e1

BaseQRankSum
type: SiteQuality
SIO_000300: -1.67e-1

QD
type: SiteQuality
SIO_000300: 1.539e1