9-139909942-G-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139909942
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139909942
    reference: chr 9
allele count: 1
allele frequency: 1.286471466062883e-5
allele num: 77732
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1662C>A
  hgvsp: ENST00000488535.1:c.1662C>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1670C>A
  hgvsp: ENST00000479446.1:c.1670C>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3708C>A
  hgvsp: ENST00000459850.1:c.3708C>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.3621C>A
  hgvsp: ENST00000341511.6:c.3621C>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.3621C>A
  hgvsp: ENST00000265662.5:c.3621C>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.3618C>A
  hgvsp: ENST00000371605.3:c.3618C>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.*697C>A
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20170
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 970
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 140
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1566
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 4808
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  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: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 880
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5108
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 37
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 26453
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 281
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1198
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 468
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 892
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 373
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 28224
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 122
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 134
  bin: 1.25e1
  variant carriers: 0
hgvs: p.Leu1207Leu
num of homozygotes: 0
population: Latino
population: Other
population: South Asian
population: African
population: European (Finnish)
population: East Asian
population: European (Non-Finnish)
reference allele: G
site quality: VQSLOD
site quality: FS
site quality: ReadPosRankSum
site quality: InbreedingCoeff
site quality: QD
site quality: BaseQRankSum
site quality: MQ
site quality: MQRankSum
site quality: ClippingRankSum
site quality: DP

9-139909951-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139909951
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139909951
    reference: chr 9
allele count: 1
allele frequency: 1.055119439520554e-5
allele num: 94776
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.*688C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3699C>T
  hgvsp: ENST00000459850.1:c.3699C>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.3612C>T
  hgvsp: ENST00000265662.5:c.3612C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1653C>T
  hgvsp: ENST00000488535.1:c.1653C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.3612C>T
  hgvsp: ENST00000341511.6:c.3612C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1661C>T
  hgvsp: ENST00000479446.1:c.1661C>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.3609C>T
  hgvsp: ENST00000371605.3:c.3609C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 7195
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 585
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 164
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12132
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1345
  bin: 3.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1381
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 34104
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3275
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 39
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1252
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 129
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 37
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 494
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 73
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 433
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 596
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12451
  bin: 2.25e1
  variant carriers: 0
hgvs: p.Gly1204Gly
num of homozygotes: 0
population: European (Finnish)
population: South Asian
population: East Asian
population: Other
population: Latino
population: African
population: European (Non-Finnish)
reference allele: G
site quality: FS
site quality: InbreedingCoeff
site quality: DP
site quality: MQRankSum
site quality: VQSLOD
site quality: MQ
site quality: ClippingRankSum
site quality: ReadPosRankSum
site quality: BaseQRankSum
site quality: QD

9-139909954-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139909954
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139909954
    reference: chr 9
allele count: 5
allele frequency: 4.990617638838983e-5
allele num: 100188
alternate allele: A
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.3609C>T
  hgvsp: ENST00000341511.6:c.3609C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1650C>T
  hgvsp: ENST00000488535.1:c.1650C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1658C>T
  hgvsp: ENST00000479446.1:c.1658C>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.3609C>T
  hgvsp: ENST00000265662.5:c.3609C>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.3606C>T
  hgvsp: ENST00000371605.3:c.3606C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3696C>T
  hgvsp: ENST00000459850.1:c.3696C>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.*685C>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 185
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 41
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 542
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1213
  bin: 1.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9416
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 7.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1539
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2699
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 36622
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7986
  bin: 2.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.75e1
  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 quality: GenotypeQuality
  all individuals: 131
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 496
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 574
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 31
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 565
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 467
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 82
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1043
  bin: 3.25e1
  variant carriers: 0
hgvs: p.Cys1203Cys
num of homozygotes: 0
population: European (Finnish)
population: African
population: Other
population: Latino
population: European (Non-Finnish)
population: East Asian
population: South Asian
reference allele: G
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: ClippingRankSum
site quality: QD
site quality: DP
site quality: BaseQRankSum
site quality: FS
site quality: ReadPosRankSum
site quality: MQ

9-139910005-G-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910005
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910005
    reference: chr 9
allele count: 1
allele frequency: 8.517597356137781e-6
allele num: 117404
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.*634C>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.1607C>A
  hgvsp: ENSP00000420084.1:p.Asp536Glu
  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.3558C>A
  hgvsp: ENSP00000344155.6:p.Asp1186Glu
  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.3555C>A
  hgvsp: ENSP00000360666.3:p.Asp1185Glu
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1599C>A
  hgvsp: ENSP00000419850.1:p.Asp533Glu
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3645C>A
  hgvsp: ENSP00000420527.1:p.Asp1215Glu
  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.3558C>A
  hgvsp: ENSP00000265662.5:p.Asp1186Glu
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 394
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12308
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 5.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 339
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2080
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 42
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 193
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43184
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 529
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1286
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1527
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 42
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 137
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 25
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 204
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 138
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 119
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 32
  bin: 9.25e1
  variant carriers: 0
hgvs: p.Asp1186Glu
num of homozygotes: 0
population: European (Finnish)
population: East Asian
population: South Asian
population: Latino
population: African
population: European (Non-Finnish)
population: Other
reference allele: G
site quality: ClippingRankSum
site quality: MQ
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: QD
site quality: BaseQRankSum
site quality: FS
site quality: VQSLOD
site quality: DP
site quality: ReadPosRankSum

9-139910011-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910011
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910011
    reference: chr 9
allele count: 468
allele frequency: 3.981013627315878e-3
allele num: 117558
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.3552G>A
  hgvsp: ENST00000341511.6:c.3552G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1601G>A
  hgvsp: ENST00000479446.1:c.1601G>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.3549G>A
  hgvsp: ENST00000371605.3:c.3549G>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.*628G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1593G>A
  hgvsp: ENST00000488535.1:c.1593G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3639G>A
  hgvsp: ENST00000459850.1:c.3639G>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.3552G>A
  hgvsp: ENST00000265662.5:c.3552G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 30
  bin: 5.25e1
  variant carriers: 26
genotype depth: GenotypeDepth
  all individuals: 576
  bin: 1.25e1
  variant carriers: 8
genotype depth: GenotypeDepth
  all individuals: 238
  bin: 3.75e1
  variant carriers: 59
genotype depth: GenotypeDepth
  all individuals: 394
  bin: 2.5e0
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 9.75e1
  variant carriers: 15
genotype depth: GenotypeDepth
  all individuals: 12432
  bin: 2.75e1
  variant carriers: 51
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 7.25e1
  variant carriers: 12
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 9.25e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 2161
  bin: 3.25e1
  variant carriers: 59
genotype depth: GenotypeDepth
  all individuals: 1214
  bin: 7.5e0
  variant carriers: 9
genotype depth: GenotypeDepth
  all individuals: 18
  bin: 6.25e1
  variant carriers: 16
genotype depth: GenotypeDepth
  all individuals: 72
  bin: 4.25e1
  variant carriers: 39
genotype depth: GenotypeDepth
  all individuals: 353
  bin: 1.75e1
  variant carriers: 25
genotype depth: GenotypeDepth
  all individuals: 30
  bin: 5.75e1
  variant carriers: 24
genotype depth: GenotypeDepth
  all individuals: 42741
  bin: 2.25e1
  variant carriers: 38
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 8.75e1
  variant carriers: 9
genotype depth: GenotypeDepth
  all individuals: 64
  bin: 4.75e1
  variant carriers: 48
genotype depth: GenotypeDepth
  all individuals: 9
  bin: 7.75e1
  variant carriers: 9
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 8.25e1
  variant carriers: 11
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 6.75e1
  variant carriers: 11
genotype quality: GenotypeQuality
  all individuals: 136
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 51331
  bin: 6.25e1
  variant carriers: 3
genotype quality: GenotypeQuality
  all individuals: 133
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 368
  bin: 7.5e0
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 1494
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 35
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 202
  bin: 5.25e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 4147
  bin: 6.75e1
  variant carriers: 3
hgvs: p.Glu1184Glu
num of homozygotes: 6
population: African
population: European (Non-Finnish)
population: South Asian
population: East Asian
population: European (Finnish)
population: Latino
population: Other
reference allele: C
site quality: VQSLOD
site quality: QD
site quality: BaseQRankSum
site quality: DP
site quality: InbreedingCoeff
site quality: FS
site quality: MQRankSum
site quality: ClippingRankSum
site quality: ReadPosRankSum
site quality: MQ

9-139910012-T-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910012
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910012
    reference: chr 9
allele count: 1
allele frequency: 8.506439374606578e-6
allele num: 117558
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.3548A>G
  hgvsp: ENSP00000360666.3:p.Glu1183Gly
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3638A>G
  hgvsp: ENSP00000420527.1:p.Glu1213Gly
  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.3551A>G
  hgvsp: ENSP00000344155.6:p.Glu1184Gly
  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.*627A>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1592A>G
  hgvsp: ENSP00000419850.1:p.Glu531Gly
  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.1600A>G
  hgvsp: ENSP00000420084.1:p.Glu534Gly
  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.3551A>G
  hgvsp: ENSP00000265662.5:p.Glu1184Gly
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 42806
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 590
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1204
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 401
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12603
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 7.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 193
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 40
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2177
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 345
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 728
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 177
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 114
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 140
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 207
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 185
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4195
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 22
  bin: 1.25e1
  variant carriers: 0
hgvs: p.Glu1184Gly
num of homozygotes: 0
population: Other
population: East Asian
population: European (Non-Finnish)
population: African
population: South Asian
population: Latino
population: European (Finnish)
reference allele: T
site quality: ReadPosRankSum
site quality: BaseQRankSum
site quality: MQ
site quality: MQRankSum
site quality: VQSLOD
site quality: FS
site quality: InbreedingCoeff
site quality: QD
site quality: DP
site quality: ClippingRankSum

9-139910016-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910016
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910016
    reference: chr 9
allele count: 1
allele frequency: 8.502533755059007e-6
allele num: 117612
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.1596G>A
  hgvsp: ENSP00000420084.1:p.Asp533Asn
  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.3547G>A
  hgvsp: ENSP00000344155.6:p.Asp1183Asn
  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.3547G>A
  hgvsp: ENSP00000265662.5:p.Asp1183Asn
  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.3544G>A
  hgvsp: ENSP00000360666.3:p.Asp1182Asn
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3634G>A
  hgvsp: ENSP00000420527.1:p.Asp1212Asn
  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.*623G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1588G>A
  hgvsp: ENSP00000419850.1:p.Asp530Asn
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: VQSRTrancheSNP99.60to99.80
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 322
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 191
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 42
  bin: 4.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 406
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 638
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12689
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 42721
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1174
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2176
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 51716
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 28
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 158
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 133
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 83
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 111
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 164
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1521
  bin: 2.25e1
  variant carriers: 0
hgvs: p.Asp1183Asn
num of homozygotes: 0
population: European (Non-Finnish)
population: European (Finnish)
population: Other
population: African
population: Latino
population: East Asian
population: South Asian
reference allele: C
site quality: ClippingRankSum
site quality: DP
site quality: MQ
site quality: MQRankSum
site quality: VQSLOD
site quality: FS
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: QD
site quality: ReadPosRankSum

9-139910044-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910044
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910044
    reference: chr 9
allele count: 2
allele frequency: 1.714383679067375e-5
allele num: 116660
alternate allele: A
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.3519C>T
  hgvsp: ENST00000341511.6:c.3519C>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.3519C>T
  hgvsp: ENST00000265662.5:c.3519C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1560C>T
  hgvsp: ENST00000488535.1:c.1560C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1568C>T
  hgvsp: ENST00000479446.1:c.1568C>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.*595C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3606C>T
  hgvsp: ENST00000459850.1:c.3606C>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.3516C>T
  hgvsp: ENST00000371605.3:c.3516C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 12574
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1495
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 508
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2108
  bin: 3.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 40377
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 952
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 191
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2073
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 5.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 44
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 33
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 165
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 339
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 177
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2792
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 485
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 541
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 353
  bin: 5.25e1
  variant carriers: 0
hgvs: p.Arg1173Arg
num of homozygotes: 0
population: East Asian
population: South Asian
population: Latino
population: Other
population: European (Finnish)
population: European (Non-Finnish)
population: African
reference allele: G
site quality: DP
site quality: BaseQRankSum
site quality: MQ
site quality: VQSLOD
site quality: MQRankSum
site quality: FS
site quality: InbreedingCoeff
site quality: QD
site quality: ClippingRankSum
site quality: ReadPosRankSum

9-139910045-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910045
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910045
    reference: chr 9
allele count: 4
allele frequency: 3.434419754782429e-5
allele num: 116468
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1559G>A
  hgvsp: ENSP00000419850.1:p.Arg520His
  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.3518G>A
  hgvsp: ENSP00000344155.6:p.Arg1173His
  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.3518G>A
  hgvsp: ENSP00000265662.5:p.Arg1173His
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3605G>A
  hgvsp: ENSP00000420527.1:p.Arg1202His
  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.1567G>A
  hgvsp: ENSP00000420084.1:p.Arg523His
  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.3515G>A
  hgvsp: ENSP00000360666.3:p.Arg1172His
  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.*594G>A
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2220
  bin: 3.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1041
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2255
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1529
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 39900
  bin: 2.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 22
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 510
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 60
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 227
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 12566
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 461
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2946
  bin: 2.25e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 58
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 48425
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 632
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 237
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 590
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3887
  bin: 6.75e1
  variant carriers: 0
hgvs: p.Arg1173His
num of homozygotes: 0
population: Other
population: African
population: South Asian
population: European (Non-Finnish)
population: Latino
population: East Asian
population: European (Finnish)
reference allele: C
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: MQRankSum
site quality: MQ
site quality: QD
site quality: FS
site quality: DP
site quality: ClippingRankSum

9-139910046-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910046
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910046
    reference: chr 9
allele count: 1
allele frequency: 8.583248931385508e-6
allele num: 116506
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: splice_region_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.3517C>T
  hgvsp: ENSP00000265662.5:p.Arg1173Cys
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: missense_variant
  consequence: splice_region_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.3517C>T
  hgvsp: ENSP00000344155.6:p.Arg1173Cys
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: splice_region_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3604C>T
  hgvsp: ENSP00000420527.1:p.Arg1202Cys
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: splice_region_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1566C>T
  hgvsp: ENSP00000420084.1:p.Arg523Cys
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: splice_region_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1558C>T
  hgvsp: ENSP00000419850.1:p.Arg520Cys
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: splice_region_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.3514C>T
  hgvsp: ENSP00000360666.3:p.Arg1172Cys
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: 3_prime_UTR_variant
  consequence: splice_region_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.*593C>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 39945
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 511
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 50
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1543
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1005
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12657
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 206
  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: 6.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2127
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2271
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 645
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 55
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 610
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 487
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 48884
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 40
  bin: 1.75e1
  variant carriers: 0
hgvs: p.Arg1173Cys
num of homozygotes: 0
population: South Asian
population: European (Finnish)
population: Latino
population: African
population: East Asian
population: Other
population: European (Non-Finnish)
reference allele: G
site quality: BaseQRankSum
site quality: VQSLOD
site quality: ReadPosRankSum
site quality: MQ
site quality: QD
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: FS
site quality: DP
site quality: ClippingRankSum

9-139910052-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910052
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910052
    reference: chr 9
allele count: 2
allele frequency: 1.723395088323998e-5
allele num: 116050
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.3515-4C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1556-4C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1564-4C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3602-4C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.3512-4C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.*591-4C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.3515-4C>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: splice region
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 49
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 546
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1277
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 197
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 15
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1725
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3028
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 38845
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12547
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2085
  bin: 3.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 47799
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3868
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 43
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 49
  bin: 9.75e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 185
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 125
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 231
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 390
  bin: 7.75e1
  variant carriers: 0
hgvs: c.3515-4C>T
num of homozygotes: 0
population: Latino
population: Other
population: European (Finnish)
population: African
population: East Asian
population: South Asian
population: European (Non-Finnish)
reference allele: G
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: FS
site quality: MQRankSum
site quality: VQSLOD
site quality: DP
site quality: ReadPosRankSum
site quality: ClippingRankSum
site quality: MQ
site quality: QD

9-139910053-G-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910053
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910053
    reference: chr 9
allele count: 1
allele frequency: 8.644088308006155e-6
allele num: 115686
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.*591-5C>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.3515-5C>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1564-5C>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.3515-5C>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.3512-5C>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1556-5C>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3602-5C>G
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: splice region
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 547
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1566
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 37893
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1884
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 45
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3577
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2091
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 196
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12481
  bin: 2.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 807
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 33
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 373
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 48
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 537
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 949
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 215
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 998
  bin: 3.25e1
  variant carriers: 0
hgvs: c.3515-5C>G
num of homozygotes: 0
population: East Asian
population: European (Finnish)
population: European (Non-Finnish)
population: African
population: Latino
population: Other
population: South Asian
reference allele: G
site quality: QD
site quality: VQSLOD
site quality: BaseQRankSum
site quality: MQRankSum
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: DP
site quality: FS
site quality: MQ
site quality: ReadPosRankSum

9-139910054-A-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910054
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910054
    reference: chr 9
allele count: 1
allele frequency: 8.64304235090752e-6
allele num: 115700
alternate allele: T
annotation: Annotation
  canonical: true
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.3515-6T>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.3515-6T>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1556-6T>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1564-6T>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3602-6T>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.3512-6T>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.*591-6T>A
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: splice region
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1546
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 548
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1890
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 189
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 37921
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3585
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12509
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2046
  bin: 3.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3717
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 537
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 46452
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4136
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 49
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 71
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 536
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 50
  bin: 2.5e0
  variant carriers: 0
hgvs: c.3515-6T>A
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: A
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: QD
site quality: DP
site quality: VQSLOD
site quality: MQ
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: FS

http://identifiers.org/exac.variant/9-139910056-A-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910056
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910056
    reference: chr 9
allele count: 1
allele frequency: 8.64304235090752e-6
allele num: 115700
alternate allele: C
annotation: Annotation
  canonical: true
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.3515-8T>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1564-8T>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1556-8T>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3602-8T>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.3515-8T>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.3512-8T>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.*591-8T>G
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: splice region
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2038
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1895
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1507
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12530
  bin: 2.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 553
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3598
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 37928
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 188
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 48
  bin: 4.25e1
  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 quality: GenotypeQuality
  all individuals: 942
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 36
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3678
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 65
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 124
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 219
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4172
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 49
  bin: 2.5e0
  variant carriers: 0
hgvs: c.3515-8T>G
num of homozygotes: 0
population: European (Finnish)
population: South Asian
population: European (Non-Finnish)
population: Other
population: African
population: East Asian
population: Latino
reference allele: A
site quality: MQ
site quality: DP
site quality: MQRankSum
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: FS
site quality: VQSLOD
site quality: QD
site quality: InbreedingCoeff
site quality: ReadPosRankSum

9-139910058-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910058
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910058
    reference: chr 9
allele count: 1
allele frequency: 8.665811639918195e-6
allele num: 115396
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.*591-10C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3602-10C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1556-10C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.3512-10C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1564-10C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.3515-10C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.3515-10C>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 15
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4044
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 561
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2017
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 37345
  bin: 2.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 197
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12298
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1725
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2040
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 49
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 55
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 409
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 357
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 287
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 553
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 118
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 44
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1069
  bin: 2.75e1
  variant carriers: 0
num of homozygotes: 0
population: European (Non-Finnish)
population: Other
population: South Asian
population: European (Finnish)
population: East Asian
population: African
population: Latino
reference allele: G
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: FS
site quality: DP
site quality: VQSLOD
site quality: QD
site quality: MQ
site quality: MQRankSum

9-139910070-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910070
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910070
    reference: chr 9
allele count: 1
allele frequency: 8.855356605210492e-6
allele num: 112926
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.3512-22C>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.*591-22C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1564-22C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1556-22C>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.3602-22C>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.3515-22C>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.3515-22C>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1979
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11339
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 31741
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 628
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 199
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7441
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3059
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3793
  bin: 1.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 7755
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 662
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 145
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 487
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 18
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 39669
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1327
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 285
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 120
  bin: 1.25e1
  variant carriers: 0
num of homozygotes: 0
population: East Asian
population: South Asian
population: European (Non-Finnish)
population: European (Finnish)
population: Other
population: African
population: Latino
reference allele: G
site quality: FS
site quality: BaseQRankSum
site quality: VQSLOD
site quality: ClippingRankSum
site quality: QD
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: InbreedingCoeff
site quality: MQ
site quality: DP

9-139910073-CAG-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910073
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910071
    reference: chr 9
allele count: 3
allele frequency: 2.691790040376851e-5
allele num: 111450
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.3515-27_3515-26delCT
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1556-27_1556-26delCT
  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.3602-27_3602-26delCT
  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.3515-27_3515-26delCT
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1564-27_1564-26delCT
  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.3512-27_3512-26delCT
  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.*591-27_*591-26delCT
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 211
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3634
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 688
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9301
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5296
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10482
  bin: 2.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 52
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1967
  bin: 3.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 28564
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 250
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1952
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 89
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 103
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2811
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 786
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 265
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3143
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1041
  bin: 5.25e1
  variant carriers: 0
num of homozygotes: 0
population: South Asian
population: East Asian
population: European (Finnish)
population: Other
population: European (Non-Finnish)
population: Latino
population: African
reference allele: CAG
site quality: BaseQRankSum
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: FS
site quality: MQ
site quality: ClippingRankSum
site quality: DP
site quality: VQSLOD
site quality: QD
site quality: InbreedingCoeff

9-139910085-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910085
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910085
    reference: chr 9
allele count: 1
allele frequency: 9.255831173639393e-6
allele num: 108040
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.3515-37C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1556-37C>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.3515-37C>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.*591-37C>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.3602-37C>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.3512-37C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1564-37C>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12571
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 185
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1643
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4826
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 22804
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 957
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9156
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7939
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 48
  bin: 4.25e1
  variant carriers: 1
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 quality: GenotypeQuality
  all individuals: 27238
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 25
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1160
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 18
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4532
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 125
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 212
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 286
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2237
  bin: 6.75e1
  variant carriers: 0
num of homozygotes: 0
population: Latino
population: European (Non-Finnish)
population: European (Finnish)
population: East Asian
population: African
population: Other
population: South Asian
reference allele: G
site quality: MQ
site quality: DP
site quality: MQRankSum
site quality: VQSLOD
site quality: FS
site quality: ClippingRankSum
site quality: QD
site quality: ReadPosRankSum
site quality: BaseQRankSum
site quality: InbreedingCoeff

9-139910085-G-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910085
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910085
    reference: chr 9
allele count: 1
allele frequency: 9.255831173639393e-6
allele num: 108040
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1564-37C>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.3602-37C>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.3515-37C>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.3512-37C>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.3515-37C>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1556-37C>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.*591-37C>A
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 7939
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 185
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 22804
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 957
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 48
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1643
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12571
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9156
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4826
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 4.75e1
  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: 2
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1200
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 125
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11982
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 48
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 212
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 18
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 430
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2237
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 286
  bin: 1.25e1
  variant carriers: 0
num of homozygotes: 0
population: East Asian
population: Other
population: South Asian
population: African
population: Latino
population: European (Finnish)
population: European (Non-Finnish)
reference allele: G
site quality: QD
site quality: ReadPosRankSum
site quality: FS
site quality: MQ
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: MQRankSum
site quality: DP

9-139910090-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910090
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910090
    reference: chr 9
allele count: 1
allele frequency: 9.46736598943442e-6
allele num: 105626
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.3601+37C>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.3514+37C>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.3514+37C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1563+37C>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.3511+37C>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.*590+37C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1555+37C>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 13383
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1145
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 180
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1503
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8540
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8687
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 55
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 21167
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  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: 5405
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 465
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2057
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1440
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 282
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1750
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 659
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 23911
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1381
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 25
  bin: 8.75e1
  variant carriers: 0
num of homozygotes: 0
population: South Asian
population: Other
population: European (Finnish)
population: Latino
population: East Asian
population: European (Non-Finnish)
population: African
reference allele: G
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: QD
site quality: DP
site quality: FS
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: MQ

9-139910092-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910092
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910092
    reference: chr 9
allele count: 26
allele frequency: 2.474634991338777e-4
allele num: 105066
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.*590+35G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1555+35G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1563+35G>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.3514+35G>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.3601+35G>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.3511+35G>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.3514+35G>A
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 5652
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1248
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20
  bin: 4.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 13525
  bin: 1.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 190
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 5.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 20881
  bin: 2.25e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 49
  bin: 4.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 1398
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 7.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8726
  bin: 1.75e1
  variant carriers: 5
genotype depth: GenotypeDepth
  all individuals: 8367
  bin: 2.75e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 5.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 6.75e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 449
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 212
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 717
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2069
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 72
  bin: 9.75e1
  variant carriers: 26
genotype quality: GenotypeQuality
  all individuals: 27
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1789
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1365
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1537
  bin: 7.5e0
  variant carriers: 0
num of homozygotes: 0
population: African
population: East Asian
population: European (Non-Finnish)
population: Other
population: European (Finnish)
population: Latino
population: South Asian
reference allele: C
site quality: MQ
site quality: BaseQRankSum
site quality: DP
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: VQSLOD
site quality: QD
site quality: FS
site quality: ReadPosRankSum
site quality: MQRankSum

9-139910093-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910093
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910093
    reference: chr 9
allele count: 297
allele frequency: 2.841670174901451e-3
allele num: 104516
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.3511+34C>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.3601+34C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1563+34C>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.*590+34C>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.3514+34C>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.3514+34C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1555+34C>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 20694
  bin: 2.25e1
  variant carriers: 61
genotype depth: GenotypeDepth
  all individuals: 209
  bin: 3.75e1
  variant carriers: 17
genotype depth: GenotypeDepth
  all individuals: 5695
  bin: 7.5e0
  variant carriers: 15
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 9.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 12
  bin: 5.75e1
  variant carriers: 7
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 9.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 9
  bin: 5.25e1
  variant carriers: 4
genotype depth: GenotypeDepth
  all individuals: 63
  bin: 4.25e1
  variant carriers: 10
genotype depth: GenotypeDepth
  all individuals: 13541
  bin: 1.25e1
  variant carriers: 31
genotype depth: GenotypeDepth
  all individuals: 1250
  bin: 2.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 21
  bin: 4.75e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.25e1
  variant carriers: 4
genotype depth: GenotypeDepth
  all individuals: 1426
  bin: 3.25e1
  variant carriers: 17
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 6.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 7.25e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 8.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 8635
  bin: 1.75e1
  variant carriers: 90
genotype depth: GenotypeDepth
  all individuals: 8506
  bin: 2.75e1
  variant carriers: 39
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 1292
  bin: 5.25e1
  variant carriers: 3
genotype quality: GenotypeQuality
  all individuals: 23967
  bin: 6.25e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 346
  bin: 7.25e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 1718
  bin: 4.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 23
  bin: 8.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 1563
  bin: 7.5e0
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 498
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 357
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4959
  bin: 3.25e1
  variant carriers: 1
num of homozygotes: 3
population: European (Non-Finnish)
population: African
population: East Asian
population: South Asian
population: Latino
population: Other
population: European (Finnish)
reference allele: G
site quality: ReadPosRankSum
site quality: QD
site quality: ClippingRankSum
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: DP
site quality: MQ
site quality: FS
site quality: BaseQRankSum
site quality: VQSLOD

9-139910094-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910094
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910094
    reference: chr 9
allele count: 1
allele frequency: 9.535251826000725e-6
allele num: 104874
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1563+33G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3601+33G>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.3514+33G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.3511+33G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.*590+33G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.3514+33G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1555+33G>A
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 20692
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8497
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1364
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8414
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1300
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13704
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5835
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 184
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18
  bin: 4.75e1
  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: 6
  bin: 5.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1509
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 211
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 521
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 364
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5059
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4431
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 257
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1566
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12657
  bin: 2.25e1
  variant carriers: 0
num of homozygotes: 0
population: European (Finnish)
population: East Asian
population: Latino
population: European (Non-Finnish)
population: Other
population: South Asian
population: African
reference allele: C
site quality: ReadPosRankSum
site quality: QD
site quality: ClippingRankSum
site quality: VQSLOD
site quality: MQRankSum
site quality: FS
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: MQ
site quality: DP

9-139910095-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910095
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910095
    reference: chr 9
allele count: 1
allele frequency: 9.567363808576184e-6
allele num: 104522
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.3601+32G>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.3511+32G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1555+32G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1563+32G>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.3514+32G>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.3514+32G>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.*590+32G>A
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 5953
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 177
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13832
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 50
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1372
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1370
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8724
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20390
  bin: 2.25e1
  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: 8157
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 19
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 583
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 17
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 959
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5205
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1297
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 497
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1492
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 367
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1642
  bin: 7.5e0
  variant carriers: 0
num of homozygotes: 0
population: European (Non-Finnish)
population: African
population: Latino
population: European (Finnish)
population: East Asian
population: Other
population: South Asian
reference allele: C
site quality: ClippingRankSum
site quality: MQ
site quality: FS
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: BaseQRankSum
site quality: VQSLOD
site quality: ReadPosRankSum
site quality: DP
site quality: QD

9-139910096-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910096
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910096
    reference: chr 9
allele count: 7
allele frequency: 6.740750727038114e-5
allele num: 103846
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.3601+31G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1555+31G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.3514+31G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1563+31G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.3511+31G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.*590+31G>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.3514+31G>A
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 13937
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8955
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7972
  bin: 2.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 7.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1415
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6021
  bin: 7.5e0
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1367
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 177
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 54
  bin: 4.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 20
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20100
  bin: 2.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5306
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 321
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1716
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1088
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2093
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1550
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 18
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 207
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4570
  bin: 2.75e1
  variant carriers: 0
num of homozygotes: 0
population: African
population: East Asian
population: South Asian
population: Other
population: Latino
population: European (Finnish)
population: European (Non-Finnish)
reference allele: C
site quality: FS
site quality: QD
site quality: MQ
site quality: VQSLOD
site quality: ClippingRankSum
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: DP
site quality: BaseQRankSum
site quality: ReadPosRankSum

9-139910097-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910097
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910097
    reference: chr 9
allele count: 307
allele frequency: 2.974575614293466e-3
allele num: 103208
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.3601+30C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1563+30C>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.3514+30C>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.3514+30C>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.3511+30C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1555+30C>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.*590+30C>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 6058
  bin: 7.5e0
  variant carriers: 14
genotype depth: GenotypeDepth
  all individuals: 195
  bin: 3.75e1
  variant carriers: 19
genotype depth: GenotypeDepth
  all individuals: 23
  bin: 4.75e1
  variant carriers: 4
genotype depth: GenotypeDepth
  all individuals: 1401
  bin: 3.25e1
  variant carriers: 38
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 13980
  bin: 1.25e1
  variant carriers: 40
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 66
  bin: 4.25e1
  variant carriers: 10
genotype depth: GenotypeDepth
  all individuals: 19928
  bin: 2.25e1
  variant carriers: 62
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 5.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 8861
  bin: 1.75e1
  variant carriers: 63
genotype depth: GenotypeDepth
  all individuals: 1436
  bin: 2.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 7.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8064
  bin: 2.75e1
  variant carriers: 64
genotype quality: GenotypeQuality
  all individuals: 1359
  bin: 4.25e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 5216
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 23575
  bin: 6.25e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 12636
  bin: 2.25e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 560
  bin: 1.25e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 338
  bin: 9.75e1
  variant carriers: 296
genotype quality: GenotypeQuality
  all individuals: 1765
  bin: 7.5e0
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 1476
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 198
  bin: 7.75e1
  variant carriers: 3
num of homozygotes: 0
population: Latino
population: Other
population: African
population: European (Non-Finnish)
population: South Asian
population: East Asian
population: European (Finnish)
reference allele: G
site quality: QD
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: VQSLOD
site quality: FS
site quality: DP
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: MQ

http://identifiers.org/exac.variant/9-139910098-C-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910098
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910098
    reference: chr 9
allele count: 1
allele frequency: 9.704215511218074e-6
allele num: 103048
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.*590+29G>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.3601+29G>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1555+29G>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.3514+29G>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.3511+29G>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.3514+29G>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1563+29G>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6280
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 19237
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1587
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9389
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 14256
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 4.25e1
  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: 17
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7700
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 175
  bin: 3.75e1
  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: 1305
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1948
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 42
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 17
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5570
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21376
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1482
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 351
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1617
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 83
  bin: 8.25e1
  variant carriers: 0
num of homozygotes: 0
population: African
population: Latino
population: European (Non-Finnish)
population: East Asian
population: Other
population: South Asian
population: European (Finnish)
reference allele: C
site quality: VQSLOD
site quality: ReadPosRankSum
site quality: DP
site quality: QD
site quality: MQRankSum
site quality: MQ
site quality: FS
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: InbreedingCoeff

http://identifiers.org/exac.variant/9-139910100-C-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910100
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910100
    reference: chr 9
allele count: 1
allele frequency: 9.70817233947537e-6
allele num: 103006
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1563+27G>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.3514+27G>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1555+27G>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.*590+27G>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.3511+27G>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.3601+27G>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.3514+27G>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 45
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9061
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1619
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 19402
  bin: 2.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 14274
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7748
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6371
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  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: 1292
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 174
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5491
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1361
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 24
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1911
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 511
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 609
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 18
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 247
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 207
  bin: 7.75e1
  variant carriers: 0
num of homozygotes: 0
population: East Asian
population: South Asian
population: European (Non-Finnish)
population: Latino
population: European (Finnish)
population: African
population: Other
reference allele: C
site quality: DP
site quality: BaseQRankSum
site quality: MQRankSum
site quality: MQ
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: FS
site quality: VQSLOD
site quality: QD
site quality: ReadPosRankSum

9-139910100-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910100
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910100
    reference: chr 9
allele count: 1
allele frequency: 9.70817233947537e-6
allele num: 103006
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1555+27G>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.3514+27G>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.*590+27G>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.3514+27G>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.3511+27G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1563+27G>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.3601+27G>A
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14274
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 45
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7748
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9061
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 19402
  bin: 2.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1619
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6371
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1292
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 174
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 609
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1395
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 207
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3687
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 342
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4615
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 18
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 511
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 336
  bin: 5.75e1
  variant carriers: 0
num of homozygotes: 0
population: South Asian
population: East Asian
population: European (Finnish)
population: Other
population: European (Non-Finnish)
population: African
population: Latino
reference allele: C
site quality: QD
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: FS
site quality: MQ
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: ClippingRankSum
site quality: DP
site quality: BaseQRankSum

http://identifiers.org/exac.variant/9-139910103-C-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910103
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910103
    reference: chr 9
allele count: 1
allele frequency: 9.753623471119521e-6
allele num: 102526
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.3511+24G>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.3601+24G>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1563+24G>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1555+24G>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.3514+24G>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.3514+24G>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.*590+24G>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  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 depth: GenotypeDepth
  all individuals: 46
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9571
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 170
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1242
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7534
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1741
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6530
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14494
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
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  variant carriers: 0
genotype depth: GenotypeDepth
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  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
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  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18647
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1981
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1388
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1039
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 22338
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 712
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 203
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3846
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12976
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4743
  bin: 2.75e1
  variant carriers: 0
num of homozygotes: 0
population: Other
population: East Asian
population: Latino
population: European (Finnish)
population: European (Non-Finnish)
population: African
population: South Asian
reference allele: C
site quality: DP
site quality: ClippingRankSum
site quality: FS
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: MQ
site quality: MQRankSum
site quality: VQSLOD
site quality: QD
site quality: BaseQRankSum

9-139910110-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910110
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910110
    reference: chr 9
allele count: 1
allele frequency: 9.916896408100121e-6
allele num: 100838
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.3514+17G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.3511+17G>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.3601+17G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1563+17G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.3514+17G>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.*590+17G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1555+17G>A
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17186
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 171
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2022
  bin: 2.5e0
  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: 4
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6970
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1187
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6903
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14589
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10828
  bin: 1.75e1
  variant carriers: 1
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: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 307
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 188
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1623
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12553
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1909
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 69
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4971
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2149
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1814
  bin: 6.75e1
  variant carriers: 0
num of homozygotes: 0
population: European (Finnish)
population: Latino
population: Other
population: European (Non-Finnish)
population: South Asian
population: East Asian
population: African
reference allele: C
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: FS
site quality: ReadPosRankSum
site quality: MQ
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: DP
site quality: QD
site quality: VQSLOD

9-139910112-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910112
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910112
    reference: chr 9
allele count: 2
allele frequency: 1.989970548435883e-5
allele num: 100504
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1563+15G>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.3514+15G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1555+15G>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.3511+15G>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.3601+15G>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.3514+15G>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.*590+15G>A
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 10656
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17388
  bin: 2.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 14548
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 52
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 166
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7012
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1189
  bin: 3.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2038
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6862
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 183
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1319
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 972
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4129
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 524
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4930
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 309
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12726
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1851
  bin: 4.75e1
  variant carriers: 0
num of homozygotes: 0
population: East Asian
population: Other
population: European (Non-Finnish)
population: Latino
population: South Asian
population: African
population: European (Finnish)
reference allele: C
site quality: ClippingRankSum
site quality: MQRankSum
site quality: MQ
site quality: DP
site quality: VQSLOD
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: FS
site quality: QD
site quality: ReadPosRankSum

9-139910113-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910113
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910113
    reference: chr 9
allele count: 16
allele frequency: 1.588814744200826e-4
allele num: 100704
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.3601+14C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1555+14C>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.3514+14C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1563+14C>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.3514+14C>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.3511+14C>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.*590+14C>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10474
  bin: 1.75e1
  variant carriers: 6
genotype depth: GenotypeDepth
  all individuals: 17553
  bin: 2.25e1
  variant carriers: 4
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14580
  bin: 1.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 167
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1151
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7072
  bin: 7.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2046
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6826
  bin: 2.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 45
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  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: 1
genotype quality: GenotypeQuality
  all individuals: 1540
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 308
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1032
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 259
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1834
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1747
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 194
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2214
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21022
  bin: 6.25e1
  variant carriers: 0
num of homozygotes: 0
population: Latino
population: European (Finnish)
population: African
population: European (Non-Finnish)
population: Other
population: East Asian
population: South Asian
reference allele: G
site quality: FS
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: MQ
site quality: BaseQRankSum
site quality: DP
site quality: QD
site quality: ClippingRankSum
site quality: VQSLOD

9-139910114-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910114
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910114
    reference: chr 9
allele count: 2
allele frequency: 1.989376728271033e-5
allele num: 100534
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.3514+13C>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.3514+13C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1555+13C>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.3601+13C>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.*590+13C>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.3511+13C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1563+13C>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7093
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1146
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17446
  bin: 2.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 14629
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2081
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10546
  bin: 1.75e1
  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: 45
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 166
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6759
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 20727
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4123
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 302
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1592
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 868
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 71
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4944
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 324
  bin: 2.5e0
  variant carriers: 0
num of homozygotes: 0
population: African
population: Other
population: Latino
population: South Asian
population: East Asian
population: European (Finnish)
population: European (Non-Finnish)
reference allele: G
site quality: MQRankSum
site quality: DP
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: MQ
site quality: QD
site quality: FS
site quality: ReadPosRankSum
site quality: VQSLOD

9-139910117-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910117
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910117
    reference: chr 9
allele count: 4
allele frequency: 3.9902637564343e-5
allele num: 100244
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.3601+10G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1555+10G>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.*590+10G>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.3514+10G>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.3514+10G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1563+10G>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.3511+10G>A
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 160
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7240
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10726
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1119
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6562
  bin: 2.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2144
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14627
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17283
  bin: 2.25e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 2282
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4155
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 296
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 308
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6014
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1789
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12808
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1591
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1293
  bin: 5.25e1
  variant carriers: 0
num of homozygotes: 0
population: Latino
population: East Asian
population: African
population: Other
population: European (Finnish)
population: European (Non-Finnish)
population: South Asian
reference allele: C
site quality: FS
site quality: QD
site quality: DP
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: VQSLOD
site quality: ClippingRankSum
site quality: ReadPosRankSum
site quality: MQ
site quality: BaseQRankSum

http://identifiers.org/exac.variant/9-139910119-CCA-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910119
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910117
    reference: chr 9
allele count: 1
allele frequency: 9.991008092716555e-6
allele num: 100090
alternate allele: C
annotation: Annotation
  canonical: true
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.3514+6_3514+7delTG
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.3514+6_3514+7delTG
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3601+6_3601+7delTG
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1563+6_1563+7delTG
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.3511+6_3511+7delTG
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000418662
  ensembl transcript: ENST00000487109
  gene symbol: ABCA2
  hgvsc: ENST00000487109.1:c.*590+6_*590+7delTG
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1555+6_1555+7delTG
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: splice region
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 166
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1115
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7276
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2173
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10670
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14637
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 17266
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6560
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  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: 3
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1586
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 332
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2296
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 830
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6006
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 16
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1789
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4131
  bin: 3.75e1
  variant carriers: 0
hgvs: c.3514+6_3514+7delTG
num of homozygotes: 0
population: Latino
population: European (Non-Finnish)
population: European (Finnish)
population: Other
population: African
population: East Asian
population: South Asian
reference allele: CCA
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: DP
site quality: FS
site quality: MQRankSum
site quality: ClippingRankSum
site quality: VQSLOD
site quality: BaseQRankSum
site quality: QD
site quality: MQ

9-139910131-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910131
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910131
    reference: chr 9
allele count: 11
allele frequency: 1.106394962885478e-4
allele num: 99422
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.1559G>A
  hgvsp: ENST00000479446.1:c.1559G>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.3507G>A
  hgvsp: ENST00000371605.3:c.3507G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1551G>A
  hgvsp: ENST00000488535.1:c.1551G>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.*586G>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.3510G>A
  hgvsp: ENST00000341511.6:c.3510G>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.3510G>A
  hgvsp: ENST00000265662.5:c.3510G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3597G>A
  hgvsp: ENST00000459850.1:c.3597G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7599
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 159
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2254
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 6.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 17250
  bin: 2.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 14467
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1135
  bin: 3.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 10598
  bin: 1.75e1
  variant carriers: 5
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15
  bin: 4.75e1
  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: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6371
  bin: 2.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 44
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 19
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 66
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 51
  bin: 9.75e1
  variant carriers: 10
genotype quality: GenotypeQuality
  all individuals: 181
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1560
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1862
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12955
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 810
  bin: 1.75e1
  variant carriers: 0
hgvs: p.Lys1170Lys
num of homozygotes: 0
population: European (Finnish)
population: East Asian
population: South Asian
population: African
population: Other
population: European (Non-Finnish)
population: Latino
reference allele: C
site quality: ClippingRankSum
site quality: MQ
site quality: DP
site quality: QD
site quality: FS
site quality: ReadPosRankSum
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: BaseQRankSum
site quality: VQSLOD

9-139910132-T-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910132
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910132
    reference: chr 9
allele count: 1
allele frequency: 1.005126143330988e-5
allele num: 99490
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1550A>G
  hgvsp: ENSP00000419850.1:p.Lys517Arg
  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.3509A>G
  hgvsp: ENSP00000344155.6:p.Lys1170Arg
  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.1558A>G
  hgvsp: ENSP00000420084.1:p.Lys520Arg
  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.3506A>G
  hgvsp: ENSP00000360666.3:p.Lys1169Arg
  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.3509A>G
  hgvsp: ENSP00000265662.5:p.Lys1170Arg
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3596A>G
  hgvsp: ENSP00000420527.1:p.Lys1199Arg
  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.*585A>G
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7633
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14430
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 45
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17374
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2247
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 161
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6390
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1133
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  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: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10459
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4976
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 20393
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 664
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1808
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 175
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 18
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5943
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12984
  bin: 2.25e1
  variant carriers: 0
hgvs: p.Lys1170Arg
num of homozygotes: 0
population: Latino
population: East Asian
population: European (Finnish)
population: European (Non-Finnish)
population: Other
population: South Asian
population: African
reference allele: T
site quality: DP
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: ClippingRankSum
site quality: MQ
site quality: FS
site quality: VQSLOD
site quality: MQRankSum
site quality: QD
site quality: BaseQRankSum

9-139910143-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910143
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910143
    reference: chr 9
allele count: 1
allele frequency: 1.004944326084335e-5
allele num: 99508
alternate allele: A
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.1547C>T
  hgvsp: ENST00000479446.1:c.1547C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.3498C>T
  hgvsp: ENST00000341511.6:c.3498C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3585C>T
  hgvsp: ENST00000459850.1:c.3585C>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.*574C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1539C>T
  hgvsp: ENST00000488535.1:c.1539C>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.3495C>T
  hgvsp: ENST00000371605.3:c.3495C>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.3498C>T
  hgvsp: ENST00000265662.5:c.3498C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 7705
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6647
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 45
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2157
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18715
  bin: 2.25e1
  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: 15
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9189
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 161
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14015
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1190
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  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: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 19
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4768
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1371
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 570
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 172
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1567
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 22161
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2203
  bin: 7.5e0
  variant carriers: 0
hgvs: p.Ile1166Ile
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: G
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: FS
site quality: VQSLOD
site quality: DP
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: QD
site quality: MQ

9-139910148-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910148
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910148
    reference: chr 9
allele count: 1
allele frequency: 1.006481742421193e-5
allele num: 99356
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.3493C>T
  hgvsp: ENSP00000265662.5:p.Leu1165Phe
  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.1542C>T
  hgvsp: ENSP00000420084.1:p.Leu515Phe
  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.3493C>T
  hgvsp: ENSP00000344155.6:p.Leu1165Phe
  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.3490C>T
  hgvsp: ENSP00000360666.3:p.Leu1164Phe
  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.*569C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3580C>T
  hgvsp: ENSP00000420527.1:p.Leu1194Phe
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1534C>T
  hgvsp: ENSP00000419850.1:p.Leu512Phe
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 6888
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 164
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13738
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9041
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 18851
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7721
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2089
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1237
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 5.25e1
  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 quality: GenotypeQuality
  all individuals: 2130
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 261
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1848
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 855
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1602
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1877
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 607
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4684
  bin: 2.75e1
  variant carriers: 0
hgvs: p.Leu1165Phe
num of homozygotes: 0
population: African
population: European (Non-Finnish)
population: South Asian
population: East Asian
population: European (Finnish)
population: Latino
population: Other
reference allele: G
site quality: BaseQRankSum
site quality: VQSLOD
site quality: FS
site quality: ClippingRankSum
site quality: MQ
site quality: ReadPosRankSum
site quality: InbreedingCoeff
site quality: QD
site quality: MQRankSum
site quality: DP

9-139910148-G-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910148
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910148
    reference: chr 9
allele count: 1
allele frequency: 1.006481742421193e-5
allele num: 99356
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.3493C>A
  hgvsp: ENSP00000344155.6:p.Leu1165Ile
  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.3493C>A
  hgvsp: ENSP00000265662.5:p.Leu1165Ile
  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.1542C>A
  hgvsp: ENSP00000420084.1:p.Leu515Ile
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1534C>A
  hgvsp: ENSP00000419850.1:p.Leu512Ile
  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.*569C>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3580C>A
  hgvsp: ENSP00000420527.1:p.Leu1194Ile
  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.3490C>A
  hgvsp: ENSP00000360666.3:p.Leu1164Ile
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18851
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13738
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6888
  bin: 2.75e1
  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: 7721
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2089
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1237
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9041
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 164
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 607
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12617
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 15
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1877
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1180
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 261
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4684
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 172
  bin: 7.75e1
  variant carriers: 0
hgvs: p.Leu1165Ile
num of homozygotes: 0
population: East Asian
population: European (Non-Finnish)
population: Latino
population: African
population: European (Finnish)
population: South Asian
population: Other
reference allele: G
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: DP
site quality: InbreedingCoeff
site quality: FS
site quality: ClippingRankSum
site quality: VQSLOD
site quality: BaseQRankSum
site quality: MQ
site quality: QD

9-139910149-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910149
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910149
    reference: chr 9
allele count: 1
allele frequency: 1.004217714400482e-5
allele num: 99580
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3579C>T
  hgvsp: ENST00000459850.1:c.3579C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1541C>T
  hgvsp: ENST00000479446.1:c.1541C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1533C>T
  hgvsp: ENST00000488535.1:c.1533C>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.3492C>T
  hgvsp: ENST00000265662.5:c.3492C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.3492C>T
  hgvsp: ENST00000341511.6:c.3492C>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.*568C>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.3489C>T
  hgvsp: ENST00000371605.3:c.3489C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 14
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 5.25e1
  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: 18950
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2073
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7714
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 165
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 4.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 8928
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13696
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6965
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1243
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 245
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5520
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4651
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 309
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1506
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 173
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12698
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1429
  bin: 4.25e1
  variant carriers: 0
hgvs: p.Asp1164Asp
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: G
site quality: MQRankSum
site quality: VQSLOD
site quality: FS
site quality: ReadPosRankSum
site quality: QD
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: MQ
site quality: ClippingRankSum
site quality: DP

9-139910160-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910160
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910160
    reference: chr 9
allele count: 1
allele frequency: 1.004782765965998e-5
allele num: 99524
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.3478G>A
  hgvsp: ENSP00000360666.3:p.Ala1160Thr
  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.3481G>A
  hgvsp: ENSP00000344155.6:p.Ala1161Thr
  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.1530G>A
  hgvsp: ENSP00000420084.1:p.Ala511Thr
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3568G>A
  hgvsp: ENSP00000420527.1:p.Ala1190Thr
  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.3481G>A
  hgvsp: ENSP00000265662.5:p.Ala1161Thr
  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.*557G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1522G>A
  hgvsp: ENSP00000419850.1:p.Ala508Thr
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1412
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12533
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8187
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7707
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 50
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1834
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 170
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20132
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7714
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1019
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 929
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 324
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 186
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 584
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2340
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21763
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5117
  bin: 3.25e1
  variant carriers: 0
hgvs: p.Ala1161Thr
num of homozygotes: 0
population: African
population: European (Non-Finnish)
population: East Asian
population: South Asian
population: Latino
population: European (Finnish)
population: Other
reference allele: C
site quality: MQ
site quality: VQSLOD
site quality: BaseQRankSum
site quality: FS
site quality: MQRankSum
site quality: DP
site quality: ReadPosRankSum
site quality: InbreedingCoeff
site quality: QD
site quality: ClippingRankSum

9-139910161-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910161
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910161
    reference: chr 9
allele count: 2
allele frequency: 1.998001998001998e-5
allele num: 100100
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3567C>T
  hgvsp: ENST00000459850.1:c.3567C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.3480C>T
  hgvsp: ENST00000341511.6:c.3480C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1521C>T
  hgvsp: ENST00000488535.1:c.1521C>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.3480C>T
  hgvsp: ENST00000265662.5:c.3480C>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.3477C>T
  hgvsp: ENST00000371605.3:c.3477C>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.*556C>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.1529C>T
  hgvsp: ENST00000479446.1:c.1529C>T(p.%3D)
  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: 7631
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7182
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 12139
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1488
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20556
  bin: 2.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1765
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 171
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8766
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 194
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1873
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 41
  bin: 9.75e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 1435
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4873
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 317
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1811
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 20
  bin: 8.75e1
  variant carriers: 0
hgvs: p.Arg1160Arg
num of homozygotes: 0
population: Latino
population: East Asian
population: Other
population: South Asian
population: African
population: European (Finnish)
population: European (Non-Finnish)
reference allele: G
site quality: FS
site quality: ReadPosRankSum
site quality: BaseQRankSum
site quality: QD
site quality: VQSLOD
site quality: ClippingRankSum
site quality: MQRankSum
site quality: MQ
site quality: DP
site quality: InbreedingCoeff

9-139910162-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910162
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910162
    reference: chr 9
allele count: 3
allele frequency: 2.991146207226609e-5
allele num: 100296
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.3479G>A
  hgvsp: ENSP00000344155.6:p.Arg1160His
  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.*555G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1520G>A
  hgvsp: ENSP00000419850.1:p.Arg507His
  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.3476G>A
  hgvsp: ENSP00000360666.3:p.Arg1159His
  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.3479G>A
  hgvsp: ENSP00000265662.5:p.Arg1160His
  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.1528G>A
  hgvsp: ENSP00000420084.1:p.Arg510His
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3566G>A
  hgvsp: ENSP00000420527.1:p.Arg1189His
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11991
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 170
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1496
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1724
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 50
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20797
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8960
  bin: 2.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7580
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6983
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 499
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 196
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1824
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 63
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1311
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 267
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 15
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 588
  bin: 1.75e1
  variant carriers: 0
hgvs: p.Arg1160His
num of homozygotes: 0
population: East Asian
population: European (Non-Finnish)
population: Latino
population: African
population: European (Finnish)
population: South Asian
population: Other
reference allele: C
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: DP
site quality: FS
site quality: VQSLOD
site quality: QD
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: MQ

9-139910163-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910163
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910163
    reference: chr 9
allele count: 4
allele frequency: 3.986446083316723e-5
allele num: 100340
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1519C>T
  hgvsp: ENSP00000419850.1:p.Arg507Cys
  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.*554C>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.3478C>T
  hgvsp: ENSP00000265662.5:p.Arg1160Cys
  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.3475C>T
  hgvsp: ENSP00000360666.3:p.Arg1159Cys
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3565C>T
  hgvsp: ENSP00000420527.1:p.Arg1189Cys
  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.1527C>T
  hgvsp: ENSP00000420084.1:p.Arg510Cys
  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.3478C>T
  hgvsp: ENSP00000344155.6:p.Arg1160Cys
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 21026
  bin: 2.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 47
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11728
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6837
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7560
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1679
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 169
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9170
  bin: 2.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1546
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4684
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2228
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3159
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 280
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 42
  bin: 9.75e1
  variant carriers: 3
genotype quality: GenotypeQuality
  all individuals: 11718
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1083
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 20
  bin: 8.75e1
  variant carriers: 0
hgvs: p.Arg1160Cys
num of homozygotes: 0
population: European (Non-Finnish)
population: Other
population: South Asian
population: African
population: European (Finnish)
population: Latino
population: East Asian
reference allele: G
site quality: ClippingRankSum
site quality: QD
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: DP
site quality: BaseQRankSum
site quality: FS
site quality: MQ
site quality: VQSLOD
site quality: ReadPosRankSum

9-139910167-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910167
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910167
    reference: chr 9
allele count: 32
allele frequency: 3.140950137416569e-4
allele num: 101880
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1515G>A
  hgvsp: ENST00000488535.1:c.1515G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3561G>A
  hgvsp: ENST00000459850.1:c.3561G>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.*550G>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.3474G>A
  hgvsp: ENST00000265662.5:c.3474G>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.3471G>A
  hgvsp: ENST00000371605.3:c.3471G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.3474G>A
  hgvsp: ENST00000341511.6:c.3474G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1523G>A
  hgvsp: ENST00000479446.1:c.1523G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 52
  bin: 4.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 180
  bin: 3.75e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10384
  bin: 2.75e1
  variant carriers: 4
genotype depth: GenotypeDepth
  all individuals: 1725
  bin: 3.25e1
  variant carriers: 5
genotype depth: GenotypeDepth
  all individuals: 7212
  bin: 7.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 22576
  bin: 2.25e1
  variant carriers: 5
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1508
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5672
  bin: 1.75e1
  variant carriers: 7
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10528
  bin: 1.25e1
  variant carriers: 7
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 921
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 23
  bin: 8.75e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 3427
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 29046
  bin: 6.25e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 376
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 383
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 316
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11264
  bin: 2.25e1
  variant carriers: 0
hgvs: p.Ala1158Ala
num of homozygotes: 0
population: African
population: European (Finnish)
population: European (Non-Finnish)
population: Latino
population: South Asian
population: Other
population: East Asian
reference allele: C
site quality: ClippingRankSum
site quality: QD
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: BaseQRankSum
site quality: VQSLOD
site quality: MQ
site quality: FS
site quality: ReadPosRankSum
site quality: DP

9-139910168-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910168
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910168
    reference: chr 9
allele count: 13
allele frequency: 1.269680040629761e-4
allele num: 102388
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3560C>T
  hgvsp: ENSP00000420527.1:p.Ala1187Val
  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.3470C>T
  hgvsp: ENSP00000360666.3:p.Ala1157Val
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1514C>T
  hgvsp: ENSP00000419850.1:p.Ala505Val
  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.3473C>T
  hgvsp: ENSP00000265662.5:p.Ala1158Val
  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.1522C>T
  hgvsp: ENSP00000420084.1:p.Ala508Val
  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.3473C>T
  hgvsp: ENSP00000344155.6:p.Ala1158Val
  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.*549C>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7097
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4992
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1390
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 23826
  bin: 2.25e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 4.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 1793
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9793
  bin: 1.25e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 181
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10740
  bin: 2.75e1
  variant carriers: 4
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 22
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11026
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 386
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2318
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 659
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 293
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1428
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1022
  bin: 4.75e1
  variant carriers: 0
hgvs: p.Ala1158Val
num of homozygotes: 0
population: European (Non-Finnish)
population: East Asian
population: African
population: Other
population: Latino
population: European (Finnish)
population: South Asian
reference allele: G
site quality: MQ
site quality: FS
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: DP
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: VQSLOD
site quality: QD

9-139910170-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910170
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910170
    reference: chr 9
allele count: 4
allele frequency: 3.876720294630743e-5
allele num: 103180
alternate allele: A
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.1520C>T
  hgvsp: ENST00000479446.1:c.1520C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1512C>T
  hgvsp: ENST00000488535.1:c.1512C>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.3468C>T
  hgvsp: ENST00000371605.3:c.3468C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.3471C>T
  hgvsp: ENST00000341511.6:c.3471C>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.*547C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3558C>T
  hgvsp: ENST00000459850.1:c.3558C>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.3471C>T
  hgvsp: ENST00000265662.5:c.3471C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6871
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 25802
  bin: 2.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 188
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 4016
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 8623
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11206
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1274
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 48
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1887
  bin: 3.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10475
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 33903
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1845
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 231
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 710
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 79
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2984
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 426
  bin: 7.25e1
  variant carriers: 0
hgvs: p.Tyr1157Tyr
num of homozygotes: 0
population: European (Finnish)
population: European (Non-Finnish)
population: African
population: East Asian
population: South Asian
population: Latino
population: Other
reference allele: G
site quality: ReadPosRankSum
site quality: MQ
site quality: QD
site quality: FS
site quality: MQRankSum
site quality: ClippingRankSum
site quality: DP
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: VQSLOD

9-139910173-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910173
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910173
    reference: chr 9
allele count: 5
allele frequency: 4.798925040790863e-5
allele num: 104190
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3555C>T
  hgvsp: ENST00000459850.1:c.3555C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1517C>T
  hgvsp: ENST00000479446.1:c.1517C>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.*544C>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.3468C>T
  hgvsp: ENST00000341511.6:c.3468C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1509C>T
  hgvsp: ENST00000488535.1:c.1509C>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.3468C>T
  hgvsp: ENST00000265662.5:c.3468C>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.3465C>T
  hgvsp: ENST00000371605.3:c.3465C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 11496
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 27935
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1949
  bin: 3.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3206
  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: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1151
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 194
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 52
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6560
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7408
  bin: 1.25e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 3168
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 392
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 82
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 140
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 557
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 200
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1169
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 540
  bin: 5.25e1
  variant carriers: 0
hgvs: p.Pro1156Pro
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: ClippingRankSum
site quality: InbreedingCoeff
site quality: FS
site quality: VQSLOD
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: DP
site quality: MQ
site quality: QD

9-139910182-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910182
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910182
    reference: chr 9
allele count: 12
allele frequency: 1.125154708772456e-4
allele num: 106652
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1500C>T
  hgvsp: ENST00000488535.1:c.1500C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1508C>T
  hgvsp: ENST00000479446.1:c.1508C>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.3459C>T
  hgvsp: ENST00000265662.5:c.3459C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3546C>T
  hgvsp: ENST00000459850.1:c.3546C>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.3456C>T
  hgvsp: ENST00000371605.3:c.3456C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.3459C>T
  hgvsp: ENST00000341511.6:c.3459C>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.*535C>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 60
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2249
  bin: 1.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 216
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5306
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  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: 2341
  bin: 3.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 1020
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 9.75e1
  variant carriers: 2
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: 14
  bin: 4.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 30676
  bin: 2.25e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 5448
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12712
  bin: 2.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 1656
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 791
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 359
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 206
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1010
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 488
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 17
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3610
  bin: 6.75e1
  variant carriers: 0
hgvs: p.Gly1153Gly
num of homozygotes: 0
population: African
population: Other
population: European (Finnish)
population: European (Non-Finnish)
population: East Asian
population: Latino
population: South Asian
reference allele: G
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: FS
site quality: QD
site quality: MQRankSum
site quality: DP
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: ClippingRankSum
site quality: MQ

9-139910185-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910185
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910185
    reference: chr 9
allele count: 2
allele frequency: 1.84304618673744e-5
allele num: 108516
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.*532G>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.3453G>A
  hgvsp: ENST00000371605.3:c.3453G>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.3456G>A
  hgvsp: ENST00000265662.5:c.3456G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1497G>A
  hgvsp: ENST00000488535.1:c.1497G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1505G>A
  hgvsp: ENST00000479446.1:c.1505G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3543G>A
  hgvsp: ENST00000459850.1:c.3543G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.3456G>A
  hgvsp: ENST00000341511.6:c.3456G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32307
  bin: 2.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1634
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2539
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 930
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13365
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4790
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4225
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 60
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 227
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6571
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 900
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 569
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1286
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 111
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 349
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1278
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 24
  bin: 9.25e1
  variant carriers: 0
hgvs: p.Ala1152Ala
num of homozygotes: 0
population: African
population: European (Finnish)
population: Latino
population: European (Non-Finnish)
population: Other
population: East Asian
population: South Asian
reference allele: C
site quality: VQSLOD
site quality: FS
site quality: MQ
site quality: ClippingRankSum
site quality: QD
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: DP
site quality: ReadPosRankSum
site quality: MQRankSum

9-139910188-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910188
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910188
    reference: chr 9
allele count: 32
allele frequency: 2.906607081221501e-4
allele num: 110094
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1494G>A
  hgvsp: ENST00000488535.1:c.1494G>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.*529G>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.3450G>A
  hgvsp: ENST00000371605.3:c.3450G>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.3453G>A
  hgvsp: ENST00000265662.5:c.3453G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3540G>A
  hgvsp: ENST00000459850.1:c.3540G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.3453G>A
  hgvsp: ENST00000341511.6:c.3453G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1502G>A
  hgvsp: ENST00000479446.1:c.1502G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 878
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2766
  bin: 3.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 4124
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33430
  bin: 2.25e1
  variant carriers: 7
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3317
  bin: 1.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 14035
  bin: 2.75e1
  variant carriers: 7
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 5.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 224
  bin: 3.75e1
  variant carriers: 5
genotype depth: GenotypeDepth
  all individuals: 63
  bin: 4.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 1278
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 9.75e1
  variant carriers: 4
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1009
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 976
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 405
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 387
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 613
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 439
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 847
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 106
  bin: 8.25e1
  variant carriers: 0
hgvs: p.Thr1151Thr
num of homozygotes: 0
population: Latino
population: East Asian
population: South Asian
population: African
population: European (Non-Finnish)
population: European (Finnish)
population: Other
reference allele: C
site quality: ClippingRankSum
site quality: VQSLOD
site quality: ReadPosRankSum
site quality: QD
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: DP
site quality: FS
site quality: MQ

9-139910194-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910194
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910194
    reference: chr 9
allele count: 2
allele frequency: 1.780436563045259e-5
allele num: 112332
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3534G>A
  hgvsp: ENST00000459850.1:c.3534G>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.3444G>A
  hgvsp: ENST00000371605.3:c.3444G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1496G>A
  hgvsp: ENST00000479446.1:c.1496G>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.3447G>A
  hgvsp: ENST00000265662.5:c.3447G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.3447G>A
  hgvsp: ENST00000341511.6:c.3447G>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.*523G>A
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1488G>A
  hgvsp: ENST00000488535.1:c.1488G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 34864
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 811
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3143
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2191
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14942
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 845
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 62
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3030
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 249
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 46691
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 72
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 356
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4053
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 71
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 772
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4388
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 633
  bin: 3.25e1
  variant carriers: 0
hgvs: p.Glu1149Glu
num of homozygotes: 0
population: Latino
population: European (Non-Finnish)
population: Other
population: African
population: South Asian
population: European (Finnish)
population: East Asian
reference allele: C
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: ClippingRankSum
site quality: FS
site quality: DP
site quality: BaseQRankSum
site quality: VQSLOD
site quality: MQ
site quality: ReadPosRankSum
site quality: QD

9-139910197-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910197
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910197
    reference: chr 9
allele count: 6
allele frequency: 5.30157103221588e-5
allele num: 113174
alternate allele: A
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.1493C>T
  hgvsp: ENST00000479446.1:c.1493C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3531C>T
  hgvsp: ENST00000459850.1:c.3531C>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.3444C>T
  hgvsp: ENST00000265662.5:c.3444C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.3444C>T
  hgvsp: ENST00000341511.6:c.3444C>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.3441C>T
  hgvsp: ENST00000371605.3:c.3441C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1485C>T
  hgvsp: ENST00000488535.1:c.1485C>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.*520C>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1817
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 65
  bin: 4.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 35385
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 254
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3138
  bin: 3.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 4.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 808
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2738
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 681
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15264
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 5.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 234
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 103
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3482
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 47
  bin: 9.75e1
  variant carriers: 6
genotype quality: GenotypeQuality
  all individuals: 117
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 774
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 534
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 657
  bin: 7.25e1
  variant carriers: 0
hgvs: p.Asp1148Asp
num of homozygotes: 0
population: Other
population: African
population: South Asian
population: Latino
population: European (Non-Finnish)
population: European (Finnish)
population: East Asian
reference allele: G
site quality: DP
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: MQ
site quality: QD
site quality: FS

9-139910202-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910202
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910202
    reference: chr 9
allele count: 1
allele frequency: 8.763781045694355e-6
allele num: 114106
alternate allele: A
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.3439C>T
  hgvsp: ENST00000341511.6:c.3439C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1488C>T
  hgvsp: ENST00000479446.1:c.1488C>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.3439C>T
  hgvsp: ENST00000265662.5:c.3439C>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.3436C>T
  hgvsp: ENST00000371605.3:c.3436C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1480C>T
  hgvsp: ENST00000488535.1:c.1480C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3526C>T
  hgvsp: ENST00000459850.1:c.3526C>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.*515C>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 61
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2267
  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: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1384
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15691
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 264
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 35909
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 526
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 844
  bin: 2.5e0
  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: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3231
  bin: 3.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 665
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 802
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 70
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 26
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 42
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 390
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 444
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 63
  bin: 1.25e1
  variant carriers: 0
hgvs: p.Leu1147Leu
num of homozygotes: 0
population: European (Non-Finnish)
population: Other
population: African
population: South Asian
population: European (Finnish)
population: Latino
population: East Asian
reference allele: G
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: MQ
site quality: VQSLOD
site quality: ClippingRankSum
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: FS
site quality: QD
site quality: DP

9-139910209-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910209
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910209
    reference: chr 9
allele count: 20
allele frequency: 1.744500462292622e-4
allele num: 114646
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.*508C>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.3429C>T
  hgvsp: ENST00000371605.3:c.3429C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3519C>T
  hgvsp: ENST00000459850.1:c.3519C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.3432C>T
  hgvsp: ENST00000341511.6:c.3432C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1481C>T
  hgvsp: ENST00000479446.1:c.1481C>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.3432C>T
  hgvsp: ENST00000265662.5:c.3432C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1473C>T
  hgvsp: ENST00000488535.1:c.1473C>T(p.%3D)
  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: 4
  bin: 6.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3329
  bin: 3.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 444
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 5.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 36019
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2002
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16073
  bin: 2.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 1115
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 261
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 870
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 62
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 7.75e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 15
  bin: 4.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 9.75e1
  variant carriers: 5
genotype quality: GenotypeQuality
  all individuals: 59
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 140
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 299
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 297
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 49173
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 26
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 70
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 830
  bin: 7.5e0
  variant carriers: 0
hgvs: p.Ala1144Ala
num of homozygotes: 0
population: European (Finnish)
population: East Asian
population: South Asian
population: Latino
population: African
population: Other
population: European (Non-Finnish)
reference allele: G
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: MQ
site quality: InbreedingCoeff
site quality: QD
site quality: DP
site quality: FS
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: VQSLOD

9-139910212-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910212
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910212
    reference: chr 9
allele count: 12
allele frequency: 1.044077470548315e-4
allele num: 114934
alternate allele: A
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.3429C>T
  hgvsp: ENST00000341511.6:c.3429C>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.3429C>T
  hgvsp: ENST00000265662.5:c.3429C>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.3426C>T
  hgvsp: ENST00000371605.3:c.3426C>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.*505C>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.1478C>T
  hgvsp: ENST00000479446.1:c.1478C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3516C>T
  hgvsp: ENST00000459850.1:c.3516C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1470C>T
  hgvsp: ENST00000488535.1:c.1470C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 5.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 266
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 36003
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 388
  bin: 1.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 16350
  bin: 2.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 893
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3422
  bin: 3.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 1836
  bin: 7.5e0
  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: 965
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 5.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 65
  bin: 4.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 246
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4776
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 136
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 78
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 245
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 33
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 844
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 163
  bin: 4.75e1
  variant carriers: 0
hgvs: p.Arg1143Arg
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: G
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: FS
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: ClippingRankSum
site quality: DP
site quality: MQ
site quality: QD

9-139910214-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910214
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910214
    reference: chr 9
allele count: 1
allele frequency: 8.682213617183837e-6
allele num: 115178
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.1476C>T
  hgvsp: ENSP00000420084.1:p.Arg493Cys
  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.3427C>T
  hgvsp: ENSP00000344155.6:p.Arg1143Cys
  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.*503C>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.3424C>T
  hgvsp: ENSP00000360666.3:p.Arg1142Cys
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3514C>T
  hgvsp: ENSP00000420527.1:p.Arg1172Cys
  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.3427C>T
  hgvsp: ENSP00000265662.5:p.Arg1143Cys
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1468C>T
  hgvsp: ENSP00000419850.1:p.Arg490Cys
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 840
  bin: 1.25e1
  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: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16540
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 891
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 36081
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 309
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1721
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3482
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 274
  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: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 63
  bin: 4.25e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 133
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 140
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 194
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4822
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 695
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2027
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 49918
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 848
  bin: 7.5e0
  variant carriers: 0
hgvs: p.Arg1143Cys
num of homozygotes: 0
population: East Asian
population: European (Non-Finnish)
population: Latino
population: South Asian
population: African
population: European (Finnish)
population: Other
reference allele: G
site quality: ClippingRankSum
site quality: ReadPosRankSum
site quality: QD
site quality: MQRankSum
site quality: FS
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: BaseQRankSum
site quality: MQ
site quality: DP

9-139910218-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910218
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910218
    reference: chr 9
allele count: 1
allele frequency: 8.666562667914651e-6
allele num: 115386
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1464C>T
  hgvsp: ENST00000488535.1:c.1464C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1472C>T
  hgvsp: ENST00000479446.1:c.1472C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3510C>T
  hgvsp: ENST00000459850.1:c.3510C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.3423C>T
  hgvsp: ENST00000341511.6:c.3423C>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.3423C>T
  hgvsp: ENST00000265662.5:c.3423C>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.3420C>T
  hgvsp: ENST00000371605.3:c.3420C>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.*499C>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 935
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 36151
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 63
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16680
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 265
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3488
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 762
  bin: 1.25e1
  variant carriers: 1
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: 4
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1597
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 270
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 127
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 61
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 112
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 66
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 127
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 50125
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 79
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 33
  bin: 8.75e1
  variant carriers: 0
hgvs: p.Gly1141Gly
num of homozygotes: 0
population: European (Non-Finnish)
population: African
population: East Asian
population: Latino
population: South Asian
population: European (Finnish)
population: Other
reference allele: G
site quality: VQSLOD
site quality: ClippingRankSum
site quality: FS
site quality: MQ
site quality: QD
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: DP
site quality: ReadPosRankSum

9-139910220-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910220
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910220
    reference: chr 9
allele count: 2
allele frequency: 1.731421843617979e-5
allele num: 115512
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1462G>A
  hgvsp: ENSP00000419850.1:p.Gly488Ser
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3508G>A
  hgvsp: ENSP00000420527.1:p.Gly1170Ser
  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.3421G>A
  hgvsp: ENSP00000265662.5:p.Gly1141Ser
  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.1470G>A
  hgvsp: ENSP00000420084.1:p.Gly491Ser
  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.3421G>A
  hgvsp: ENSP00000344155.6:p.Gly1141Ser
  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.3418G>A
  hgvsp: ENSP00000360666.3:p.Gly1140Ser
  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.*497G>A
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 269
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14
  bin: 4.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16800
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3520
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1534
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 5.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 36115
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 943
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 242
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 730
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 62
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 133
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 120
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 50252
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 183
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 77
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 99
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 98
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1817
  bin: 2.25e1
  variant carriers: 0
hgvs: p.Gly1141Ser
num of homozygotes: 0
population: Latino
population: Other
population: European (Non-Finnish)
population: East Asian
population: African
population: South Asian
population: European (Finnish)
reference allele: C
site quality: FS
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: VQSLOD
site quality: DP
site quality: QD
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: MQ
site quality: ReadPosRankSum

9-139910221-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910221
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910221
    reference: chr 9
allele count: 2
allele frequency: 1.731691689611582e-5
allele num: 115494
alternate allele: A
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.3420C>T
  hgvsp: ENST00000341511.6:c.3420C>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.*496C>T
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1461C>T
  hgvsp: ENST00000488535.1:c.1461C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1469C>T
  hgvsp: ENST00000479446.1:c.1469C>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.3420C>T
  hgvsp: ENST00000265662.5:c.3420C>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.3417C>T
  hgvsp: ENST00000371605.3:c.3417C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3507C>T
  hgvsp: ENST00000459850.1:c.3507C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 36028
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 281
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1498
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 966
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16852
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 729
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 6.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 66
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 246
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3550
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 70
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 121
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 43
  bin: 9.75e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 97
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 26
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 83
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 154
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 455
  bin: 7.75e1
  variant carriers: 0
hgvs: p.Gly1140Gly
num of homozygotes: 0
population: Latino
population: European (Non-Finnish)
population: South Asian
population: African
population: European (Finnish)
population: East Asian
population: Other
reference allele: G
site quality: QD
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: MQ
site quality: ReadPosRankSum
site quality: DP
site quality: MQRankSum
site quality: FS
site quality: BaseQRankSum
site quality: ClippingRankSum

9-139910227-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910227
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910227
    reference: chr 9
allele count: 11
allele frequency: 9.509154722592023e-5
allele num: 115678
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.3411C>T
  hgvsp: ENST00000371605.3:c.3411C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3501C>T
  hgvsp: ENST00000459850.1:c.3501C>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.*490C>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.3414C>T
  hgvsp: ENST00000341511.6:c.3414C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1455C>T
  hgvsp: ENST00000488535.1:c.1455C>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.3414C>T
  hgvsp: ENST00000265662.5:c.3414C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1463C>T
  hgvsp: ENST00000479446.1:c.1463C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 5.75e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 173
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1414
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1016
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 36062
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 9.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 274
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 7.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3560
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 653
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 60
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17038
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 6.75e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 132
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1662
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4919
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 67
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 964
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 50459
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 51
  bin: 9.75e1
  variant carriers: 11
genotype quality: GenotypeQuality
  all individuals: 89
  bin: 5.25e1
  variant carriers: 0
hgvs: p.Phe1138Phe
num of homozygotes: 0
population: East Asian
population: European (Non-Finnish)
population: European (Finnish)
population: Other
population: Latino
population: African
population: South Asian
reference allele: G
site quality: FS
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: QD
site quality: DP
site quality: VQSLOD
site quality: MQ
site quality: BaseQRankSum
site quality: ClippingRankSum

9-139910233-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910233
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910233
    reference: chr 9
allele count: 7
allele frequency: 6.047411707789066e-5
allele num: 115752
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.3405C>T
  hgvsp: ENST00000371605.3:c.3405C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.3408C>T
  hgvsp: ENST00000341511.6:c.3408C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1449C>T
  hgvsp: ENST00000488535.1:c.1449C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1457C>T
  hgvsp: ENST00000479446.1:c.1457C>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.*484C>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.3408C>T
  hgvsp: ENST00000265662.5:c.3408C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3495C>T
  hgvsp: ENST00000459850.1:c.3495C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 17118
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1345
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 651
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 8.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 35999
  bin: 2.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 66
  bin: 4.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 165
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1070
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 279
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3584
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 7.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 13
  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: 9.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 34
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 708
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 161
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 47
  bin: 9.75e1
  variant carriers: 7
genotype quality: GenotypeQuality
  all individuals: 109
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1025
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 62
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4906
  bin: 6.75e1
  variant carriers: 0
hgvs: p.Ile1136Ile
num of homozygotes: 0
population: Other
population: Latino
population: European (Finnish)
population: South Asian
population: East Asian
population: African
population: European (Non-Finnish)
reference allele: G
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: VQSLOD
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: DP
site quality: MQ
site quality: FS
site quality: QD
site quality: ReadPosRankSum

9-139910241-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910241
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910241
    reference: chr 9
allele count: 2
allele frequency: 1.727772210511766e-5
allele num: 115756
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.3400G>A
  hgvsp: ENSP00000265662.5:p.Val1134Met
  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.3397G>A
  hgvsp: ENSP00000360666.3:p.Val1133Met
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1441G>A
  hgvsp: ENSP00000419850.1:p.Val481Met
  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.1449G>A
  hgvsp: ENSP00000420084.1:p.Val484Met
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3487G>A
  hgvsp: ENSP00000420527.1:p.Val1163Met
  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.3400G>A
  hgvsp: ENSP00000344155.6:p.Val1134Met
  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.*476G>A
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 277
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 35979
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17188
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3594
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1121
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 617
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1315
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 63
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 141
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 7.25e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 53
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 68
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 30
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 96
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 50655
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 121
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 54
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1073
  bin: 7.5e0
  variant carriers: 0
hgvs: p.Val1134Met
num of homozygotes: 0
population: European (Non-Finnish)
population: Latino
population: South Asian
population: East Asian
population: African
population: Other
population: European (Finnish)
reference allele: C
site quality: MQRankSum
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: FS
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: QD
site quality: DP
site quality: VQSLOD
site quality: MQ

9-139910242-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910242
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910242
    reference: chr 9
allele count: 15
allele frequency: 1.295694837951766e-4
allele num: 115768
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1440C>T
  hgvsp: ENST00000488535.1:c.1440C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1448C>T
  hgvsp: ENST00000479446.1:c.1448C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.3399C>T
  hgvsp: ENST00000341511.6:c.3399C>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.3399C>T
  hgvsp: ENST00000265662.5:c.3399C>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.3396C>T
  hgvsp: ENST00000371605.3:c.3396C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3486C>T
  hgvsp: ENST00000459850.1:c.3486C>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.*475C>T
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 1127
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 8.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1300
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3606
  bin: 3.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 7.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 610
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17189
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 135
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 277
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 70
  bin: 4.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 9.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 7.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 35976
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 6.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 707
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 52
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 450
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 108
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1074
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 27
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 75
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 112
  bin: 1.75e1
  variant carriers: 0
hgvs: p.Ser1133Ser
num of homozygotes: 0
population: Other
population: European (Non-Finnish)
population: East Asian
population: European (Finnish)
population: South Asian
population: Latino
population: African
reference allele: G
site quality: InbreedingCoeff
site quality: DP
site quality: ClippingRankSum
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: MQRankSum
site quality: FS
site quality: QD
site quality: MQ
site quality: BaseQRankSum

9-139910245-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910245
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910245
    reference: chr 9
allele count: 2
allele frequency: 1.727891626637177e-5
allele num: 115748
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.3393G>A
  hgvsp: ENST00000371605.3:c.3393G>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.3396G>A
  hgvsp: ENST00000265662.5:c.3396G>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.*472G>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.1445G>A
  hgvsp: ENST00000479446.1:c.1445G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.3396G>A
  hgvsp: ENST00000341511.6:c.3396G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3483G>A
  hgvsp: ENST00000459850.1:c.3483G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1437G>A
  hgvsp: ENST00000488535.1:c.1437G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 63
  bin: 4.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3608
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1293
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1153
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17208
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 35959
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 132
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 613
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 272
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 17
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 36
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 452
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 45
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 92
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 37
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1099
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 35
  bin: 5.75e1
  variant carriers: 0
hgvs: p.Leu1132Leu
num of homozygotes: 0
population: Other
population: Latino
population: European (Finnish)
population: European (Non-Finnish)
population: South Asian
population: East Asian
population: African
reference allele: C
site quality: VQSLOD
site quality: MQ
site quality: BaseQRankSum
site quality: MQRankSum
site quality: ClippingRankSum
site quality: FS
site quality: DP
site quality: QD
site quality: InbreedingCoeff
site quality: ReadPosRankSum

9-139910252-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910252
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910252
    reference: chr 9
allele count: 2
allele frequency: 1.72995415621486e-5
allele num: 115610
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.3389G>A
  hgvsp: ENSP00000265662.5:p.Arg1130His
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3476G>A
  hgvsp: ENSP00000420527.1:p.Arg1159His
  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.3389G>A
  hgvsp: ENSP00000344155.6:p.Arg1130His
  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.*465G>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.3386G>A
  hgvsp: ENSP00000360666.3:p.Arg1129His
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1430G>A
  hgvsp: ENSP00000419850.1:p.Arg477His
  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.1438G>A
  hgvsp: ENSP00000420084.1:p.Arg480His
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 279
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 65
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 153
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1269
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3611
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 35870
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1239
  bin: 2.5e0
  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: 1
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 660
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 17160
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 77
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 67
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 92
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 447
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 25
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 55
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 80
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 118
  bin: 2.75e1
  variant carriers: 0
hgvs: p.Arg1130His
num of homozygotes: 0
population: East Asian
population: Other
population: European (Non-Finnish)
population: Latino
population: South Asian
population: European (Finnish)
population: African
reference allele: C
site quality: MQRankSum
site quality: ClippingRankSum
site quality: MQ
site quality: DP
site quality: VQSLOD
site quality: QD
site quality: ReadPosRankSum
site quality: FS
site quality: InbreedingCoeff
site quality: BaseQRankSum

9-139910261-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910261
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910261
    reference: chr 9
allele count: 1
allele frequency: 8.66265874322147e-6
allele num: 115438
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.3380G>A
  hgvsp: ENSP00000344155.6:p.Gly1127Asp
  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.3377G>A
  hgvsp: ENSP00000360666.3:p.Gly1126Asp
  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.1429G>A
  hgvsp: ENSP00000420084.1:p.Gly477Asp
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3467G>A
  hgvsp: ENSP00000420527.1:p.Gly1156Asp
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1421G>A
  hgvsp: ENSP00000419850.1:p.Gly474Asp
  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.3380G>A
  hgvsp: ENSP00000265662.5:p.Gly1127Asp
  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.*456G>A
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 3605
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 163
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 64
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 277
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 35773
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 687
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1325
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17155
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1242
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 131
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 83
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4927
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1495
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 74
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 109
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 52
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 44
  bin: 5.75e1
  variant carriers: 0
hgvs: p.Gly1127Asp
num of homozygotes: 0
population: East Asian
population: African
population: South Asian
population: European (Non-Finnish)
population: Latino
population: Other
population: European (Finnish)
reference allele: C
site quality: MQ
site quality: ReadPosRankSum
site quality: FS
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: VQSLOD
site quality: MQRankSum
site quality: DP
site quality: QD

9-139910266-C-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910266
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910266
    reference: chr 9
allele count: 1
allele frequency: 8.666412451901412e-6
allele num: 115388
alternate allele: G
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.*451G>C
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1416G>C
  hgvsp: ENST00000488535.1:c.1416G>C(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1424G>C
  hgvsp: ENST00000479446.1:c.1424G>C(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3462G>C
  hgvsp: ENST00000459850.1:c.3462G>C(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000265662
  ensembl transcript: ENST00000265662
  gene symbol: ABCA2
  hgvsc: ENST00000265662.5:c.3375G>C
  hgvsp: ENST00000265662.5:c.3375G>C(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.3375G>C
  hgvsp: ENST00000341511.6:c.3375G>C(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.3372G>C
  hgvsp: ENST00000371605.3:c.3372G>C(p.%3D)
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 3592
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 35737
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1230
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 65
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1369
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 151
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 697
  bin: 1.25e1
  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: 0
genotype depth: GenotypeDepth
  all individuals: 280
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17156
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 131
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 47
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 127
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4917
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 14
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 20
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1553
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 88
  bin: 1.25e1
  variant carriers: 0
hgvs: p.Ser1125Ser
num of homozygotes: 0
population: Other
population: Latino
population: European (Non-Finnish)
population: African
population: European (Finnish)
population: East Asian
population: South Asian
reference allele: C
site quality: FS
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: ClippingRankSum
site quality: QD
site quality: MQ
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: VQSLOD
site quality: DP

9-139910266-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910266
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910266
    reference: chr 9
allele count: 1
allele frequency: 8.666412451901412e-6
allele num: 115388
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.3375G>A
  hgvsp: ENST00000265662.5:c.3375G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420084
  ensembl transcript: ENST00000479446
  gene symbol: ABCA2
  hgvsc: ENST00000479446.1:c.1424G>A
  hgvsp: ENST00000479446.1:c.1424G>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.*451G>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.3372G>A
  hgvsp: ENST00000371605.3:c.3372G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.3375G>A
  hgvsp: ENST00000341511.6:c.3375G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3462G>A
  hgvsp: ENST00000459850.1:c.3462G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1416G>A
  hgvsp: ENST00000488535.1:c.1416G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 151
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 697
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 65
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3592
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 35737
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1230
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 280
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1369
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17156
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 6.25e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 4917
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 26
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 88
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 29
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 66
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 718
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 90
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 131
  bin: 2.75e1
  variant carriers: 0
hgvs: p.Ser1125Ser
num of homozygotes: 0
population: European (Non-Finnish)
population: European (Finnish)
population: Latino
population: African
population: South Asian
population: Other
population: East Asian
reference allele: C
site quality: ReadPosRankSum
site quality: InbreedingCoeff
site quality: FS
site quality: MQRankSum
site quality: BaseQRankSum
site quality: QD
site quality: DP
site quality: MQ
site quality: VQSLOD
site quality: ClippingRankSum

9-139910272-T-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 139910272
    reference: chr 9
  end: Position
    type: ExactPosition
    position: 139910272
    reference: chr 9
allele count: 7
allele frequency: 6.072804247492799e-5
allele num: 115268
alternate allele: C
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.*445A>G
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000344155
  ensembl transcript: ENST00000341511
  gene symbol: ABCA2
  hgvsc: ENST00000341511.6:c.3369A>G
  hgvsp: ENST00000341511.6:c.3369A>G(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000360666
  ensembl transcript: ENST00000371605
  gene symbol: ABCA2
  hgvsc: ENST00000371605.3:c.3366A>G
  hgvsp: ENST00000371605.3:c.3366A>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.1418A>G
  hgvsp: ENST00000479446.1:c.1418A>G(p.%3D)
  variant of: http://identifiers.org/hgnc/32
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000107331
  ensembl protein: ENSP00000420527
  ensembl transcript: ENST00000459850
  gene symbol: ABCA2
  hgvsc: ENST00000459850.1:c.3456A>G
  hgvsp: ENST00000459850.1:c.3456A>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.3369A>G
  hgvsp: ENST00000265662.5:c.3369A>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: ENSP00000419850
  ensembl transcript: ENST00000488535
  gene symbol: ABCA2
  hgvsc: ENST00000488535.1:c.1410A>G
  hgvsp: ENST00000488535.1:c.1410A>G(p.%3D)
  variant of: http://identifiers.org/hgnc/32
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1427
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 7.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 699
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 5.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 6.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 14
  bin: 4.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 277
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1208
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3583
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 149
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 63
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 35714
  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: 6.75e1
  variant carriers: 0
hgvs: p.Thr1123Thr
num of homozygotes: 0
reference allele: T

GenotypeQuality
all individuals: 638
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 37
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 57
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 473
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1739
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 20531
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 245
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 692
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2108
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1830
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 106
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 25
bin: 9.25e1
variant carriers: 0

Latino
type: Population
allele count: 1
allele frequency: 1.545595054095827e-4
allele num: 6470
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 568
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 12282
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5842
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 3268
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5248
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 44054
num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: -7.8e-3

FS
type: SiteQuality
SIO_000300: 0.0e0

ReadPosRankSum
type: SiteQuality
SIO_000300: -5.31e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -3.9e-3

QD
type: SiteQuality
SIO_000300: 1.067e1

BaseQRankSum
type: SiteQuality
SIO_000300: -2.082e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

MQRankSum
type: SiteQuality
SIO_000300: -5.31e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -6.12e-1

DP
type: SiteQuality
SIO_000300: 9.76083e5

GenotypeQuality
all individuals: 37744
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 68
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 401
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 936
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 549
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 450
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1125
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 33
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 58
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 147
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 376
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 2910
bin: 6.75e1
variant carriers: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 4236
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 7.326007326007326e-5
allele num: 13650
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6792
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 696
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8862
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7262
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 53278
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 8.759e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.0e-3

DP
type: SiteQuality
SIO_000300: 1.127983e6

MQRankSum
type: SiteQuality
SIO_000300: -4.09e-1

VQSLOD
type: SiteQuality
SIO_000300: -1.099e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

ClippingRankSum
type: SiteQuality
SIO_000300: -1.148e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.03e0

BaseQRankSum
type: SiteQuality
SIO_000300: -3.523e0

QD
type: SiteQuality
SIO_000300: 8.24e0

GenotypeQuality
all individuals: 970
bin: 2.75e1
variant carriers: 1

GenotypeQuality
all individuals: 9721
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 836
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 75
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 429
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 40616
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 516
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 3144
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 122
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 37
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 368
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 62
bin: 9.75e1
variant carriers: 4

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 4574
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7702
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 728
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9548
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 3
allele frequency: 5.340168749332479e-5
allele num: 56178
num of homozygotes: 0

East Asian
type: Population
allele count: 2
allele frequency: 2.751031636863824e-4
allele num: 7270
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 14188
num of homozygotes: 0

MQRankSum
type: SiteQuality
SIO_000300: 3.01e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.8e-3

VQSLOD
type: SiteQuality
SIO_000300: 2.74e0

ClippingRankSum
type: SiteQuality
SIO_000300: -3.72e-1

QD
type: SiteQuality
SIO_000300: 1.186e1

DP
type: SiteQuality
SIO_000300: 1.181089e6

BaseQRankSum
type: SiteQuality
SIO_000300: 1.23e0

FS
type: SiteQuality
SIO_000300: 1.421e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 5.99e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

GenotypeQuality
all individuals: 370
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 37
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 66
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 51619
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 192
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 84
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 110
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 31
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 4214
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 181
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 728
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 541
bin: 7.75e1
variant carriers: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5980
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8538
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 6.125199068969742e-5
allele num: 16326
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11332
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9658
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 64730
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 840
num of homozygotes: 0

ClippingRankSum
type: SiteQuality
SIO_000300: -1.54e0

MQ
type: SiteQuality
SIO_000300: 5.958e1

MQRankSum
type: SiteQuality
SIO_000300: 1.12e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 7.0e-4

QD
type: SiteQuality
SIO_000300: 1.314e1

BaseQRankSum
type: SiteQuality
SIO_000300: -1.726e0

FS
type: SiteQuality
SIO_000300: 3.945e0

VQSLOD
type: SiteQuality
SIO_000300: 7.27e-1

DP
type: SiteQuality
SIO_000300: 1.359955e6

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.51e0

GenotypeQuality
all individuals: 146
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 186
bin: 2.75e1
variant carriers: 2

GenotypeQuality
all individuals: 28
bin: 1.75e1
variant carriers: 1

GenotypeQuality
all individuals: 38
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 181
bin: 8.25e1
variant carriers: 2

GenotypeQuality
all individuals: 712
bin: 7.25e1
variant carriers: 3

GenotypeQuality
all individuals: 118
bin: 3.75e1
variant carriers: 1

GenotypeQuality
all individuals: 21
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 499
bin: 9.75e1
variant carriers: 453

GenotypeQuality
all individuals: 84
bin: 4.25e1
variant carriers: 2

GenotypeQuality
all individuals: 28
bin: 9.25e1
variant carriers: 1

GenotypeQuality
all individuals: 514
bin: 7.75e1
variant carriers: 0

African
type: Population
allele count: 415
allele frequency: 4.273064250411861e-2
allele num: 9712
num of homozygotes: 6

European (Non-Finnish)
type: Population
allele count: 18
allele frequency: 2.778892765615833e-4
allele num: 64774
num of homozygotes: 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: 8542
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5992
num of homozygotes: 0

Latino
type: Population
allele count: 32
allele frequency: 2.819383259911894e-3
allele num: 11350
num of homozygotes: 0

Other
type: Population
allele count: 3
allele frequency: 3.562945368171022e-3
allele num: 842
num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: 6.09e0

QD
type: SiteQuality
SIO_000300: 1.167e1

BaseQRankSum
type: SiteQuality
SIO_000300: -8.22e-1

DP
type: SiteQuality
SIO_000300: 1.371283e6

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.52e-2

FS
type: SiteQuality
SIO_000300: 0.0e0

MQRankSum
type: SiteQuality
SIO_000300: 2.71e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -2.4e-2

ReadPosRankSum
type: SiteQuality
SIO_000300: 4.25e-1

MQ
type: SiteQuality
SIO_000300: 5.959e1

GenotypeQuality
all individuals: 51648
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 38
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 529
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 385
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 53
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 33
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 27
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 145
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 82
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 29
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 154
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1509
bin: 2.25e1
variant carriers: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 842
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8544
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 64782
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9704
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 6.119202056051891e-5
allele num: 16342
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11350
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5994
num of homozygotes: 0

ReadPosRankSum
type: SiteQuality
SIO_000300: 6.63e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 1.45e0

MQ
type: SiteQuality
SIO_000300: 5.903e1

MQRankSum
type: SiteQuality
SIO_000300: 2.32e-1

VQSLOD
type: SiteQuality
SIO_000300: -1.22e-2

FS
type: SiteQuality
SIO_000300: 3.394e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.2e-3

QD
type: SiteQuality
SIO_000300: 1.483e1

DP
type: SiteQuality
SIO_000300: 1.363346e6

ClippingRankSum
type: SiteQuality
SIO_000300: -1.19e-1

GenotypeQuality
all individuals: 529
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 185
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 29
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 25
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 725
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 174
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 384
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 4201
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 38
bin: 8.75e1
variant carriers: 0

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

GenotypeQuality
all individuals: 52
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 115
bin: 3.75e1
variant carriers: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 64806
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6002
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 842
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 1.030502885408079e-4
allele num: 9704
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11356
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8542
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16360
num of homozygotes: 0

ClippingRankSum
type: SiteQuality
SIO_000300: -2.92e0

DP
type: SiteQuality
SIO_000300: 1.363875e6

MQ
type: SiteQuality
SIO_000300: 5.953e1

MQRankSum
type: SiteQuality
SIO_000300: -1.421e0

VQSLOD
type: SiteQuality
SIO_000300: -2.85e0

FS
type: SiteQuality
SIO_000300: 5.633e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -4.0e-4

BaseQRankSum
type: SiteQuality
SIO_000300: -7.8e-2

QD
type: SiteQuality
SIO_000300: 2.44e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 2.34e-1

GenotypeQuality
all individuals: 530
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 649
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 454
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 36
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 49225
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 205
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 44
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 51
bin: 9.75e1
variant carriers: 2

GenotypeQuality
all individuals: 240
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 36
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3982
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 25
bin: 9.25e1
variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8500
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16306
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11296
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 842
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5902
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 2
allele frequency: 3.110323162576591e-5
allele num: 64302
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9512
num of homozygotes: 0

DP
type: SiteQuality
SIO_000300: 1.339025e6

BaseQRankSum
type: SiteQuality
SIO_000300: -2.262e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

VQSLOD
type: SiteQuality
SIO_000300: 3.83e-1

MQRankSum
type: SiteQuality
SIO_000300: -6.74e-1

FS
type: SiteQuality
SIO_000300: 0.0e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 3.0e-4

QD
type: SiteQuality
SIO_000300: 1.028e1

ClippingRankSum
type: SiteQuality
SIO_000300: -3.5e-2

ReadPosRankSum
type: SiteQuality
SIO_000300: 4.36e-1

GenotypeQuality
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bin: 8.25e1
variant carriers: 0

GenotypeQuality
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bin: 8.75e1
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GenotypeQuality
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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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GenotypeQuality
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GenotypeQuality
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bin: 9.75e1
variant carriers: 3

GenotypeQuality
all individuals: 24
bin: 9.25e1
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GenotypeQuality
all individuals: 484
bin: 5.25e1
variant carriers: 0

Other
type: Population
allele count: 1
allele frequency: 1.193317422434368e-3
allele num: 838
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9474
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16290
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 64216
num of homozygotes: 0

Latino
type: Population
allele count: 1
allele frequency: 8.866820358219543e-5
allele num: 11278
num of homozygotes: 0

East Asian
type: Population
allele count: 1
allele frequency: 1.178411501296253e-4
allele num: 8486
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 1
allele frequency: 1.698946653075094e-4
allele num: 5886
num of homozygotes: 0

InbreedingCoeff
type: SiteQuality
SIO_000300: 8.0e-4

BaseQRankSum
type: SiteQuality
SIO_000300: 2.93e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 6.35e-1

VQSLOD
type: SiteQuality
SIO_000300: 7.07e-1

MQRankSum
type: SiteQuality
SIO_000300: -3.73e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

QD
type: SiteQuality
SIO_000300: 1.085e1

FS
type: SiteQuality
SIO_000300: 0.0e0

DP
type: SiteQuality
SIO_000300: 1.338278e6

ClippingRankSum
type: SiteQuality
SIO_000300: -2.12e-1

GenotypeQuality
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variant carriers: 1

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
all individuals: 143
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variant carriers: 0

GenotypeQuality
all individuals: 25
bin: 9.25e1
variant carriers: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16292
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5896
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11288
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9472
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8486
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 838
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.556807921038702e-5
allele num: 64234
num of homozygotes: 0

BaseQRankSum
type: SiteQuality
SIO_000300: 3.77e0

VQSLOD
type: SiteQuality
SIO_000300: 9.92e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.25e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

QD
type: SiteQuality
SIO_000300: 1.345e1

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.2e-3

MQRankSum
type: SiteQuality
SIO_000300: -1.281e0

FS
type: SiteQuality
SIO_000300: 9.85e-1

DP
type: SiteQuality
SIO_000300: 1.337002e6

ClippingRankSum
type: SiteQuality
SIO_000300: -1.194e0

GenotypeQuality
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bin: 1.25e1
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: 251
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GenotypeQuality
all individuals: 459
bin: 3.75e1
variant carriers: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11252
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 832
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5864
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9406
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8460
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16256
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 2
allele frequency: 3.125976867771179e-5
allele num: 63980
num of homozygotes: 0

BaseQRankSum
type: SiteQuality
SIO_000300: -7.7e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -9.0e-4

FS
type: SiteQuality
SIO_000300: 3.915e0

MQRankSum
type: SiteQuality
SIO_000300: 9.88e-1

VQSLOD
type: SiteQuality
SIO_000300: -6.117e-1

DP
type: SiteQuality
SIO_000300: 1.323623e6

ReadPosRankSum
type: SiteQuality
SIO_000300: 5.45e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 4.06e-1

MQ
type: SiteQuality
SIO_000300: 5.883e1

QD
type: SiteQuality
SIO_000300: 1.431e1

GenotypeQuality
all individuals: 85
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 583
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 545
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GenotypeQuality
all individuals: 46107
bin: 6.25e1
variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8440
num of homozygotes: 0

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

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.567791295622727e-5
allele num: 63784
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9350
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11218
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 830
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16228
num of homozygotes: 0

QD
type: SiteQuality
SIO_000300: 1.306e1

VQSLOD
type: SiteQuality
SIO_000300: 6.53e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 7.97e-1

MQRankSum
type: SiteQuality
SIO_000300: -3.34e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 7.7e-2

InbreedingCoeff
type: SiteQuality
SIO_000300: -5.999999999999999e-4

DP
type: SiteQuality
SIO_000300: 1.313974e6

FS
type: SiteQuality
SIO_000300: 2.366e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

ReadPosRankSum
type: SiteQuality
SIO_000300: -7.46e-1

GenotypeQuality
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bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 540
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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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variant carriers: 0

GenotypeQuality
all individuals: 34
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GenotypeQuality
all individuals: 49
bin: 9.75e1
variant carriers: 1

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 63790
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5844
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8440
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9348
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 830
num of homozygotes: 0

Latino
type: Population
allele count: 1
allele frequency: 8.914244963451596e-5
allele num: 11218
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16230
num of homozygotes: 0

ClippingRankSum
type: SiteQuality
SIO_000300: 2.09e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -7.0e-4

BaseQRankSum
type: SiteQuality
SIO_000300: 1.88e0

QD
type: SiteQuality
SIO_000300: 1.142e1

DP
type: SiteQuality
SIO_000300: 1.313516e6

VQSLOD
type: SiteQuality
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MQ
type: SiteQuality
SIO_000300: 5.855e1

MQRankSum
type: SiteQuality
SIO_000300: -1.71e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 7.41e-1

FS
type: SiteQuality
SIO_000300: 3.848e0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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bin: 9.75e1
variant carriers: 1

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5846
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 6.160670280926565e-5
allele num: 16232
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 63786
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 834
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9346
num of homozygotes: 0

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

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11218
num of homozygotes: 0

MQ
type: SiteQuality
SIO_000300: 5.839e1

DP
type: SiteQuality
SIO_000300: 1.313687e6

MQRankSum
type: SiteQuality
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ClippingRankSum
type: SiteQuality
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BaseQRankSum
type: SiteQuality
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FS
type: SiteQuality
SIO_000300: 0.0e0

VQSLOD
type: SiteQuality
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QD
type: SiteQuality
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InbreedingCoeff
type: SiteQuality
SIO_000300: -8.0e-4

ReadPosRankSum
type: SiteQuality
SIO_000300: -2.2e-2

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

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.570894467309686e-5
allele num: 63658
num of homozygotes: 0

Other
type: Population
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allele frequency: 0.0e0
allele num: 830
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16206
num of homozygotes: 0

European (Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 5820
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8408
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African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9282
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Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11192
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BaseQRankSum
type: SiteQuality
SIO_000300: -1.262e0

ClippingRankSum
type: SiteQuality
SIO_000300: -1.385e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.2e-3

ReadPosRankSum
type: SiteQuality
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FS
type: SiteQuality
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DP
type: SiteQuality
SIO_000300: 1.305085e6

VQSLOD
type: SiteQuality
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QD
type: SiteQuality
SIO_000300: 1.029e1

MQ
type: SiteQuality
SIO_000300: 6.0e1

MQRankSum
type: SiteQuality
SIO_000300: 7.69e-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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East Asian
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allele count: 0
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allele num: 8202
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16028
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European (Non-Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 62272
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European (Finnish)
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allele count: 0
allele frequency: 0.0e0
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Other
type: Population
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allele num: 820
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African
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allele frequency: 1.114578689255461e-4
allele num: 8972
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10968
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 3.096e0

BaseQRankSum
type: SiteQuality
SIO_000300: -8.87e-1

VQSLOD
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ClippingRankSum
type: SiteQuality
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QD
type: SiteQuality
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MQRankSum
type: SiteQuality
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ReadPosRankSum
type: SiteQuality
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InbreedingCoeff
type: SiteQuality
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MQ
type: SiteQuality
SIO_000300: 5.739e1

DP
type: SiteQuality
SIO_000300: 1.240177e6

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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variant carriers: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 15940
num of homozygotes: 0

East Asian
type: Population
allele count: 1
allele frequency: 1.243781094527363e-4
allele num: 8040
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: 808
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European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 61414
num of homozygotes: 0

Latino
type: Population
allele count: 2
allele frequency: 1.844678103670909e-4
allele num: 10842
num of homozygotes: 0

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

BaseQRankSum
type: SiteQuality
SIO_000300: -3.21e0

MQRankSum
type: SiteQuality
SIO_000300: 9.21e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: -3.4e-1

FS
type: SiteQuality
SIO_000300: 2.832e0

MQ
type: SiteQuality
SIO_000300: 5.986e1

ClippingRankSum
type: SiteQuality
SIO_000300: 1.34e0

DP
type: SiteQuality
SIO_000300: 1.201884e6

VQSLOD
type: SiteQuality
SIO_000300: 2.39e0

QD
type: SiteQuality
SIO_000300: 1.704e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.7e-3

GenotypeQuality
all individuals: 375
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 430
bin: 5.75e1
variant carriers: 0

GenotypeQuality
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bin: 7.5e0
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GenotypeQuality
all individuals: 11982
bin: 2.25e1
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GenotypeQuality
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bin: 2.75e1
variant carriers: 0

GenotypeQuality
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bin: 4.75e1
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: 82
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 48
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 1200
bin: 5.25e1
variant carriers: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10528
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 59470
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5394
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7680
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 1.185114956150747e-4
allele num: 8438
num of homozygotes: 0

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

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 15752
num of homozygotes: 0

MQ
type: SiteQuality
SIO_000300: 5.944e1

DP
type: SiteQuality
SIO_000300: 1.125617e6

MQRankSum
type: SiteQuality
SIO_000300: 4.54e-1

VQSLOD
type: SiteQuality
SIO_000300: 1.58e0

FS
type: SiteQuality
SIO_000300: 1.109e0

ClippingRankSum
type: SiteQuality
SIO_000300: 9.95e-1

QD
type: SiteQuality
SIO_000300: 1.502e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.61e0

BaseQRankSum
type: SiteQuality
SIO_000300: -1.775e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 5.8e-3

GenotypeQuality
all individuals: 375
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 3050
bin: 3.75e1
variant carriers: 0

GenotypeQuality
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bin: 1.75e1
variant carriers: 0

GenotypeQuality
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bin: 3.25e1
variant carriers: 0

GenotypeQuality
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bin: 7.5e0
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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: 6.25e1
variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 4037
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 25
bin: 8.75e1
variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7680
num of homozygotes: 0

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

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 15752
num of homozygotes: 0

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

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10528
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5394
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.681520094165125e-5
allele num: 59470
num of homozygotes: 0

QD
type: SiteQuality
SIO_000300: 1.502e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.61e0

FS
type: SiteQuality
SIO_000300: 1.109e0

MQ
type: SiteQuality
SIO_000300: 5.944e1

VQSLOD
type: SiteQuality
SIO_000300: 1.58e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 5.8e-3

ClippingRankSum
type: SiteQuality
SIO_000300: 9.95e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -1.775e0

MQRankSum
type: SiteQuality
SIO_000300: 4.54e-1

DP
type: SiteQuality
SIO_000300: 1.125617e6

GenotypeQuality
all individuals: 1846
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 90
bin: 8.25e1
variant carriers: 0

GenotypeQuality
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GenotypeQuality
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bin: 2.25e1
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GenotypeQuality
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bin: 3.75e1
variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 1

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
all individuals: 566
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GenotypeQuality
all individuals: 17
bin: 9.25e1
variant carriers: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 15608
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 760
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5246
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10266
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7430
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.721407422708807e-5
allele num: 58092
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8224
num of homozygotes: 0

InbreedingCoeff
type: SiteQuality
SIO_000300: -4.8e-3

ClippingRankSum
type: SiteQuality
SIO_000300: 7.02e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 5.8e-1

QD
type: SiteQuality
SIO_000300: 1.545e1

DP
type: SiteQuality
SIO_000300: 1.098133e6

FS
type: SiteQuality
SIO_000300: 3.174e0

MQRankSum
type: SiteQuality
SIO_000300: 4.54e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: -2.64e-1

VQSLOD
type: SiteQuality
SIO_000300: 5.81e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

GenotypeQuality
all individuals: 241
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 89
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 706
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variant carriers: 0

GenotypeQuality
all individuals: 17
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 340
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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
all individuals: 3553
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 5095
bin: 3.25e1
variant carriers: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8152
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7344
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 57756
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 754
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5242
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10240
num of homozygotes: 0

South Asian
type: Population
allele count: 26
allele frequency: 1.669020413403518e-3
allele num: 15578
num of homozygotes: 0

MQ
type: SiteQuality
SIO_000300: 6.0e1

BaseQRankSum
type: SiteQuality
SIO_000300: 1.14e0

DP
type: SiteQuality
SIO_000300: 1.089684e6

InbreedingCoeff
type: SiteQuality
SIO_000300: -5.3e-3

ClippingRankSum
type: SiteQuality
SIO_000300: -1.37e-1

VQSLOD
type: SiteQuality
SIO_000300: 2.8e0

QD
type: SiteQuality
SIO_000300: 1.335e1

FS
type: SiteQuality
SIO_000300: 0.0e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.23e-1

MQRankSum
type: SiteQuality
SIO_000300: 3.67e-1

GenotypeQuality
all individuals: 498
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 209
bin: 7.75e1
variant carriers: 2

GenotypeQuality
all individuals: 4339
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variant carriers: 1

GenotypeQuality
all individuals: 688
bin: 1.75e1
variant carriers: 3

GenotypeQuality
all individuals: 17
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variant carriers: 1

GenotypeQuality
all individuals: 12357
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variant carriers: 0

GenotypeQuality
all individuals: 325
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variant carriers: 285

GenotypeQuality
all individuals: 3465
bin: 3.75e1
variant carriers: 3

GenotypeQuality
all individuals: 86
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variant carriers: 3

GenotypeQuality
all individuals: 2007
bin: 6.75e1
variant carriers: 1

GenotypeQuality
all individuals: 1372
bin: 4.25e1
variant carriers: 1

European (Non-Finnish)
type: Population
allele count: 10
allele frequency: 1.741068319520858e-4
allele num: 57436
num of homozygotes: 0

African
type: Population
allele count: 267
allele frequency: 3.306911072578648e-2
allele num: 8074
num of homozygotes: 3

East Asian
type: Population
allele count: 3
allele frequency: 4.106214070626882e-4
allele num: 7306
num of homozygotes: 0

South Asian
type: Population
allele count: 2
allele frequency: 1.286504567091213e-4
allele num: 15546
num of homozygotes: 0

Latino
type: Population
allele count: 13
allele frequency: 1.279527559055118e-3
allele num: 10160
num of homozygotes: 0

Other
type: Population
allele count: 2
allele frequency: 2.666666666666667e-3
allele num: 750
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5244
num of homozygotes: 0

ReadPosRankSum
type: SiteQuality
SIO_000300: 4.24e-1

QD
type: SiteQuality
SIO_000300: 1.295e1

ClippingRankSum
type: SiteQuality
SIO_000300: 1.01e-1

MQRankSum
type: SiteQuality
SIO_000300: 2.59e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 4.0e-4

DP
type: SiteQuality
SIO_000300: 1.091792e6

MQ
type: SiteQuality
SIO_000300: 6.0e1

FS
type: SiteQuality
SIO_000300: 0.0e0

BaseQRankSum
type: SiteQuality
SIO_000300: -1.179e0

VQSLOD
type: SiteQuality
SIO_000300: 5.94e0

GenotypeQuality
all individuals: 27
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 951
bin: 5.25e1
variant carriers: 0

GenotypeQuality
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GenotypeQuality
all individuals: 416
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
all individuals: 88
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variant carriers: 0

GenotypeQuality
all individuals: 17
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GenotypeQuality
all individuals: 2114
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variant carriers: 0

GenotypeQuality
all individuals: 24801
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GenotypeQuality
all individuals: 43
bin: 9.75e1
variant carriers: 1

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5244
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7346
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10192
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 57676
num of homozygotes: 0

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

South Asian
type: Population
allele count: 1
allele frequency: 6.417661404184315e-5
allele num: 15582
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8078
num of homozygotes: 0

ReadPosRankSum
type: SiteQuality
SIO_000300: 2.2e-1

QD
type: SiteQuality
SIO_000300: 1.488e1

ClippingRankSum
type: SiteQuality
SIO_000300: 8.599999999999999e-2

VQSLOD
type: SiteQuality
SIO_000300: 1.99e0

MQRankSum
type: SiteQuality
SIO_000300: 2.9e-2

FS
type: SiteQuality
SIO_000300: 1.172e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -5.2e-3

BaseQRankSum
type: SiteQuality
SIO_000300: -4.239e0

MQ
type: SiteQuality
SIO_000300: 5.955e1

DP
type: SiteQuality
SIO_000300: 1.08515e6

GenotypeQuality
all individuals: 12676
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 211
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variant carriers: 0

GenotypeQuality
all individuals: 4524
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 440
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variant carriers: 0

GenotypeQuality
all individuals: 211
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GenotypeQuality
all individuals: 2123
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GenotypeQuality
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GenotypeQuality
all individuals: 3532
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GenotypeQuality
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variant carriers: 1

GenotypeQuality
all individuals: 88
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 27
bin: 8.75e1
variant carriers: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 57478
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8044
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10148
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5228
num of homozygotes: 0

East Asian
type: Population
allele count: 1
allele frequency: 1.370238421485339e-4
allele num: 7298
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 750
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 15576
num of homozygotes: 0

ClippingRankSum
type: SiteQuality
SIO_000300: -1.134e0

MQ
type: SiteQuality
SIO_000300: 5.344e1

FS
type: SiteQuality
SIO_000300: 6.264e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -5.0e-3

MQRankSum
type: SiteQuality
SIO_000300: 2.89e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -2.637e0

VQSLOD
type: SiteQuality
SIO_000300: -1.099e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 5.36e-1

DP
type: SiteQuality
SIO_000300: 1.078072e6

QD
type: SiteQuality
SIO_000300: 1.364e1

GenotypeQuality
all individuals: 493
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 672
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 81
bin: 8.25e1
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GenotypeQuality
all individuals: 362
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GenotypeQuality
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GenotypeQuality
all individuals: 23185
bin: 6.25e1
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GenotypeQuality
all individuals: 1351
bin: 4.25e1
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GenotypeQuality
all individuals: 3618
bin: 3.75e1
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GenotypeQuality
all individuals: 12591
bin: 2.25e1
variant carriers: 1

GenotypeQuality
all individuals: 26
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 49
bin: 9.75e1
variant carriers: 8

African
type: Population
allele count: 1
allele frequency: 1.258178158027177e-4
allele num: 7948
num of homozygotes: 0

East Asian
type: Population
allele count: 2
allele frequency: 2.783189535207348e-4
allele num: 7186
num of homozygotes: 0

South Asian
type: Population
allele count: 3
allele frequency: 1.929508618471829e-4
allele num: 15548
num of homozygotes: 0

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

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10090
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5204
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.750577690637911e-5
allele num: 57124
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 0.0e0

QD
type: SiteQuality
SIO_000300: 1.279e1

MQ
type: SiteQuality
SIO_000300: 6.0e1

VQSLOD
type: SiteQuality
SIO_000300: 2.14e0

ClippingRankSum
type: SiteQuality
SIO_000300: -6.1e-2

MQRankSum
type: SiteQuality
SIO_000300: 2.33e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -6.0e-3

DP
type: SiteQuality
SIO_000300: 1.0729e6

BaseQRankSum
type: SiteQuality
SIO_000300: 9.19e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: -4.1e-1

GenotypeQuality
all individuals: 641
bin: 1.75e1
variant carriers: 1

GenotypeQuality
all individuals: 955
bin: 5.25e1
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GenotypeQuality
all individuals: 380
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GenotypeQuality
all individuals: 443
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GenotypeQuality
all individuals: 2005
bin: 6.75e1
variant carriers: 3

GenotypeQuality
all individuals: 24
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variant carriers: 6

GenotypeQuality
all individuals: 340
bin: 7.25e1
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GenotypeQuality
all individuals: 81
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variant carriers: 5

GenotypeQuality
all individuals: 26
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variant carriers: 1

GenotypeQuality
all individuals: 4495
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3527
bin: 3.75e1
variant carriers: 0

Latino
type: Population
allele count: 3
allele frequency: 3.013863773357444e-4
allele num: 9954
num of homozygotes: 0

Other
type: Population
allele count: 2
allele frequency: 2.680965147453083e-3
allele num: 746
num of homozygotes: 0

African
type: Population
allele count: 4
allele frequency: 5.058168942842691e-4
allele num: 7908
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 266
allele frequency: 4.682274247491638e-3
allele num: 56810
num of homozygotes: 0

South Asian
type: Population
allele count: 13
allele frequency: 8.396847952460922e-4
allele num: 15482
num of homozygotes: 0

East Asian
type: Population
allele count: 4
allele frequency: 5.602240896358543e-4
allele num: 7140
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 15
allele frequency: 2.902476780185759e-3
allele num: 5168
num of homozygotes: 0

QD
type: SiteQuality
SIO_000300: 1.326e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 4.39e-1

MQRankSum
type: SiteQuality
SIO_000300: 2.38e-1

VQSLOD
type: SiteQuality
SIO_000300: 4.19e0

FS
type: SiteQuality
SIO_000300: 5.679999999999999e-1

DP
type: SiteQuality
SIO_000300: 1.073759e6

ClippingRankSum
type: SiteQuality
SIO_000300: 0.0e0

BaseQRankSum
type: SiteQuality
SIO_000300: -1.294e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -8.200000000000001e-3

MQ
type: SiteQuality
SIO_000300: 6.0e1

GenotypeQuality
all individuals: 546
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 12557
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 3835
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 275
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 204
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 4682
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1844
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 900
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 25
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1265
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1398
bin: 5.25e1
variant carriers: 0

African
type: Population
allele count: 1
allele frequency: 1.266784899923993e-4
allele num: 7894
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9980
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 56666
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7108
num of homozygotes: 0

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

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 15528
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5128
num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: -9.534e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: -1.733e0

DP
type: SiteQuality
SIO_000300: 1.058154e6

QD
type: SiteQuality
SIO_000300: 1.543e1

MQRankSum
type: SiteQuality
SIO_000300: 9.83e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

FS
type: SiteQuality
SIO_000300: 5.008e0

ClippingRankSum
type: SiteQuality
SIO_000300: 1.36e0

BaseQRankSum
type: SiteQuality
SIO_000300: -2.107e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -5.8e-3

GenotypeQuality
all individuals: 4615
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3687
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 336
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 977
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 43
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 342
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 12920
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1975
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1395
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 81
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 23276
bin: 6.25e1
variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7092
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 15502
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.764477538200939e-5
allele num: 56674
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9984
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5138
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7874
num of homozygotes: 0

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

DP
type: SiteQuality
SIO_000300: 1.058343e6

BaseQRankSum
type: SiteQuality
SIO_000300: -1.796e0

MQRankSum
type: SiteQuality
SIO_000300: -3.5e-2

MQ
type: SiteQuality
SIO_000300: 6.0e1

InbreedingCoeff
type: SiteQuality
SIO_000300: 6.6e-3

ClippingRankSum
type: SiteQuality
SIO_000300: 5.21e-1

FS
type: SiteQuality
SIO_000300: 1.101e0

VQSLOD
type: SiteQuality
SIO_000300: 8.98e-1

QD
type: SiteQuality
SIO_000300: 1.043e1

ReadPosRankSum
type: SiteQuality
SIO_000300: -1.01e-1

GenotypeQuality
all individuals: 24
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 81
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1911
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 1361
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1975
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 23276
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 247
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 43
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 977
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 5491
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 12920
bin: 2.25e1
variant carriers: 0

South Asian
type: Population
allele count: 1
allele frequency: 6.450780544445878e-5
allele num: 15502
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7092
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5138
num of homozygotes: 0

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

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 56674
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7874
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9984
num of homozygotes: 0

QD
type: SiteQuality
SIO_000300: 1.043e1

MQRankSum
type: SiteQuality
SIO_000300: -3.5e-2

InbreedingCoeff
type: SiteQuality
SIO_000300: 6.6e-3

FS
type: SiteQuality
SIO_000300: 1.101e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

ReadPosRankSum
type: SiteQuality
SIO_000300: -1.01e-1

VQSLOD
type: SiteQuality
SIO_000300: 8.98e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 5.21e-1

DP
type: SiteQuality
SIO_000300: 1.058343e6

BaseQRankSum
type: SiteQuality
SIO_000300: -1.796e0

GenotypeQuality
all individuals: 540
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 237
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 5657
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 20
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 73
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variant carriers: 0

GenotypeQuality
all individuals: 444
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variant carriers: 0

GenotypeQuality
all individuals: 1910
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variant carriers: 0

GenotypeQuality
all individuals: 1533
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 17
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 42
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 315
bin: 7.25e1
variant carriers: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 738
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7038
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9976
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5128
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 56362
num of homozygotes: 0

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

South Asian
type: Population
allele count: 1
allele frequency: 6.467468632777131e-5
allele num: 15462
num of homozygotes: 0

DP
type: SiteQuality
SIO_000300: 1.047412e6

ClippingRankSum
type: SiteQuality
SIO_000300: 4.0e-2

FS
type: SiteQuality
SIO_000300: 9.58e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -5.8e-3

ReadPosRankSum
type: SiteQuality
SIO_000300: -3.83e-1

MQ
type: SiteQuality
SIO_000300: 5.951e1

MQRankSum
type: SiteQuality
SIO_000300: -6.12e-1

VQSLOD
type: SiteQuality
SIO_000300: 6.77e-1

QD
type: SiteQuality
SIO_000300: 1.171e1

BaseQRankSum
type: SiteQuality
SIO_000300: -4.961e0

GenotypeQuality
all individuals: 724
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1165
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 6029
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 316
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 22
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 42
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 19028
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1173
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1640
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 4202
bin: 3.75e1
variant carriers: 0

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

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5036
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9744
num of homozygotes: 0

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

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 55392
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 6.493506493506494e-5
allele num: 15400
num of homozygotes: 0

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

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7654
num of homozygotes: 0

BaseQRankSum
type: SiteQuality
SIO_000300: 2.04e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -1.429e0

FS
type: SiteQuality
SIO_000300: 5.18e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.1e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -5.8e-3

MQRankSum
type: SiteQuality
SIO_000300: -2.04e-1

DP
type: SiteQuality
SIO_000300: 1.023227e6

QD
type: SiteQuality
SIO_000300: 9.619999999999999e0

VQSLOD
type: SiteQuality
SIO_000300: 4.96e-1

GenotypeQuality
all individuals: 373
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 2226
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 1607
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1796
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 735
bin: 1.25e1
variant carriers: 0

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

GenotypeQuality
all individuals: 5930
bin: 3.25e1
variant carriers: 0

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

GenotypeQuality
all individuals: 20188
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 45
bin: 9.75e1
variant carriers: 2

GenotypeQuality
all individuals: 69
bin: 8.25e1
variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6856
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 722
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 2
allele frequency: 3.621613791105316e-5
allele num: 55224
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9682
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 15350
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7632
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5038
num of homozygotes: 0

ClippingRankSum
type: SiteQuality
SIO_000300: 7.28e-1

MQRankSum
type: SiteQuality
SIO_000300: 5.24e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

DP
type: SiteQuality
SIO_000300: 1.023594e6

VQSLOD
type: SiteQuality
SIO_000300: 1.81e0

BaseQRankSum
type: SiteQuality
SIO_000300: -3.65e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -6.3e-3

FS
type: SiteQuality
SIO_000300: 3.918e0

QD
type: SiteQuality
SIO_000300: 1.451e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 8.74e-1

GenotypeQuality
all individuals: 5907
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 686
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 848
bin: 1.75e1
variant carriers: 0

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

GenotypeQuality
all individuals: 12873
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 4922
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 4093
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 70
bin: 8.25e1
variant carriers: 1

GenotypeQuality
all individuals: 308
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 58
bin: 9.75e1
variant carriers: 16

GenotypeQuality
all individuals: 22
bin: 8.75e1
variant carriers: 0

Latino
type: Population
allele count: 1
allele frequency: 1.024380249948781e-4
allele num: 9762
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 3
allele frequency: 5.947660586835844e-4
allele num: 5044
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 1.307531380753138e-4
allele num: 7648
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 10
allele frequency: 1.809496236247829e-4
allele num: 55264
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 724
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6874
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 6.498570314530803e-5
allele num: 15388
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 1.116e0

MQRankSum
type: SiteQuality
SIO_000300: 5.73e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -6.2e-3

ReadPosRankSum
type: SiteQuality
SIO_000300: 3.18e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

BaseQRankSum
type: SiteQuality
SIO_000300: 4.33e-1

DP
type: SiteQuality
SIO_000300: 1.022734e6

QD
type: SiteQuality
SIO_000300: 1.394e1

ClippingRankSum
type: SiteQuality
SIO_000300: -4.23e-1

VQSLOD
type: SiteQuality
SIO_000300: 2.41e0

GenotypeQuality
all individuals: 706
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 12826
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 300
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 5972
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 194
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1093
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 15
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variant carriers: 0

GenotypeQuality
all individuals: 44
bin: 9.75e1
variant carriers: 2

GenotypeQuality
all individuals: 1831
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 2241
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 1754
bin: 4.75e1
variant carriers: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7594
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 726
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9732
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 15374
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6888
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5016
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 2
allele frequency: 3.622925874936599e-5
allele num: 55204
num of homozygotes: 0

MQRankSum
type: SiteQuality
SIO_000300: 7.39e-1

DP
type: SiteQuality
SIO_000300: 1.020318e6

ClippingRankSum
type: SiteQuality
SIO_000300: -3.26e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -5.5e-3

BaseQRankSum
type: SiteQuality
SIO_000300: -1.936e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

QD
type: SiteQuality
SIO_000300: 1.041e1

FS
type: SiteQuality
SIO_000300: 2.241e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.81e-1

VQSLOD
type: SiteQuality
SIO_000300: 4.88e-1

GenotypeQuality
all individuals: 705
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 191
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 909
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 68
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 4986
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 20206
bin: 6.25e1
variant carriers: 1

GenotypeQuality
all individuals: 421
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 44
bin: 9.75e1
variant carriers: 3

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

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

GenotypeQuality
all individuals: 1842
bin: 4.75e1
variant carriers: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9746
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6848
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7600
num of homozygotes: 0

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

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5038
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 4
allele frequency: 7.277755540191405e-5
allele num: 54962
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 15330
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 8.87e-1

QD
type: SiteQuality
SIO_000300: 9.59e0

DP
type: SiteQuality
SIO_000300: 1.014904e6

InbreedingCoeff
type: SiteQuality
SIO_000300: -6.0e-3

MQRankSum
type: SiteQuality
SIO_000300: 2.12e-1

VQSLOD
type: SiteQuality
SIO_000300: 1.22e0

ClippingRankSum
type: SiteQuality
SIO_000300: 2.54e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 2.12e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

BaseQRankSum
type: SiteQuality
SIO_000300: -2.451e0

GenotypeQuality
all individuals: 1142
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 12859
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 19
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 706
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 66
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 4975
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 297
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 42
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 1814
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 397
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 173
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 20466
bin: 6.25e1
variant carriers: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9708
num of homozygotes: 0

European (Non-Finnish)
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allele count: 1
allele frequency: 1.820962925194843e-5
allele num: 54916
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5026
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 714
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7590
num of homozygotes: 0

East Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 6808
num of homozygotes: 0

South Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 15328
num of homozygotes: 0

InbreedingCoeff
type: SiteQuality
SIO_000300: -5.9e-3

ReadPosRankSum
type: SiteQuality
SIO_000300: 3.86e-1

DP
type: SiteQuality
SIO_000300: 1.013895e6

FS
type: SiteQuality
SIO_000300: 0.0e0

MQRankSum
type: SiteQuality
SIO_000300: 1.22e0

ClippingRankSum
type: SiteQuality
SIO_000300: -9.65e-1

VQSLOD
type: SiteQuality
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BaseQRankSum
type: SiteQuality
SIO_000300: -1.109e0

QD
type: SiteQuality
SIO_000300: 1.798e1

MQ
type: SiteQuality
SIO_000300: 5.833e1

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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variant carriers: 0

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

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5024
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6766
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 15290
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7508
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 722
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 11
allele frequency: 2.018348623853211e-4
allele num: 54500
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9612
num of homozygotes: 0

ClippingRankSum
type: SiteQuality
SIO_000300: -5.43e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

DP
type: SiteQuality
SIO_000300: 1.00833e6

QD
type: SiteQuality
SIO_000300: 1.461e1

FS
type: SiteQuality
SIO_000300: 0.0e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 5.46e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -6.1e-3

MQRankSum
type: SiteQuality
SIO_000300: 4.0e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -2.383e0

VQSLOD
type: SiteQuality
SIO_000300: 5.54e0

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: 1321
bin: 5.25e1
variant carriers: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9640
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6770
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5036
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 54532
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 724
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 15292
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 1.334044823906083e-4
allele num: 7496
num of homozygotes: 0

DP
type: SiteQuality
SIO_000300: 1.008786e6

InbreedingCoeff
type: SiteQuality
SIO_000300: -5.7e-3

ReadPosRankSum
type: SiteQuality
SIO_000300: -3.18e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -2.12e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

FS
type: SiteQuality
SIO_000300: 0.0e0

VQSLOD
type: SiteQuality
SIO_000300: 5.01e-1

MQRankSum
type: SiteQuality
SIO_000300: -5.29e-1

QD
type: SiteQuality
SIO_000300: 1.417e1

BaseQRankSum
type: SiteQuality
SIO_000300: 4.23e-1

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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variant carriers: 1

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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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: 1887
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variant carriers: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.834054728193089e-5
allele num: 54524
num of homozygotes: 0

Other
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: 9656
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5084
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6780
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7460
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 15284
num of homozygotes: 0

MQRankSum
type: SiteQuality
SIO_000300: -4.1e-2

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.69e0

FS
type: SiteQuality
SIO_000300: 1.871e0

VQSLOD
type: SiteQuality
SIO_000300: -3.228e-1

DP
type: SiteQuality
SIO_000300: 1.020451e6

ClippingRankSum
type: SiteQuality
SIO_000300: -2.188e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -4.9e-3

BaseQRankSum
type: SiteQuality
SIO_000300: -2.436e0

QD
type: SiteQuality
SIO_000300: 7.88e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

GenotypeQuality
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bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 12617
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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: 43
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variant carriers: 1

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7450
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 54390
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 6.53765690376569e-5
allele num: 15296
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6782
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5090
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9628
num of homozygotes: 0

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

BaseQRankSum
type: SiteQuality
SIO_000300: 5.0e-2

VQSLOD
type: SiteQuality
SIO_000300: -5.765e-1

FS
type: SiteQuality
SIO_000300: 1.574e0

ClippingRankSum
type: SiteQuality
SIO_000300: 6.48e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 6.53e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 7.4e-3

QD
type: SiteQuality
SIO_000300: 6.36e0

MQRankSum
type: SiteQuality
SIO_000300: 1.77e-1

DP
type: SiteQuality
SIO_000300: 1.025794e6

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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GenotypeQuality
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GenotypeQuality
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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

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6782
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.838573267144696e-5
allele num: 54390
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9628
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7450
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5090
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 15296
num of homozygotes: 0

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

MQRankSum
type: SiteQuality
SIO_000300: 1.77e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 6.53e-1

DP
type: SiteQuality
SIO_000300: 1.025794e6

InbreedingCoeff
type: SiteQuality
SIO_000300: 7.4e-3

FS
type: SiteQuality
SIO_000300: 1.574e0

ClippingRankSum
type: SiteQuality
SIO_000300: 6.48e-1

VQSLOD
type: SiteQuality
SIO_000300: -5.765e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 5.0e-2

MQ
type: SiteQuality
SIO_000300: 6.0e1

QD
type: SiteQuality
SIO_000300: 6.36e0

GenotypeQuality
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variant carriers: 0

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

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 722
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 15302
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.836075205640423e-5
allele num: 54464
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9676
num of homozygotes: 0

African
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allele count: 0
allele frequency: 0.0e0
allele num: 7466
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6844
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5106
num of homozygotes: 0

MQRankSum
type: SiteQuality
SIO_000300: 1.2e-2

VQSLOD
type: SiteQuality
SIO_000300: 1.02e0

FS
type: SiteQuality
SIO_000300: 1.659e0

ReadPosRankSum
type: SiteQuality
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QD
type: SiteQuality
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BaseQRankSum
type: SiteQuality
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InbreedingCoeff
type: SiteQuality
SIO_000300: -4.7e-3

MQ
type: SiteQuality
SIO_000300: 6.0e1

ClippingRankSum
type: SiteQuality
SIO_000300: 6.2e-2

DP
type: SiteQuality
SIO_000300: 1.027884e6

GenotypeQuality
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variant carriers: 0

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

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7394
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.840942562592047e-5
allele num: 54320
num of homozygotes: 0

East Asian
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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

Latino
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allele frequency: 0.0e0
allele num: 9694
num of homozygotes: 0

European (Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 5222
num of homozygotes: 0

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

MQ
type: SiteQuality
SIO_000300: 5.938e1

VQSLOD
type: SiteQuality
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BaseQRankSum
type: SiteQuality
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FS
type: SiteQuality
SIO_000300: 1.091e0

MQRankSum
type: SiteQuality
SIO_000300: 9.81e-1

DP
type: SiteQuality
SIO_000300: 1.058803e6

ReadPosRankSum
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InbreedingCoeff
type: SiteQuality
SIO_000300: -4.5e-3

QD
type: SiteQuality
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ClippingRankSum
type: SiteQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

Latino
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allele frequency: 0.0e0
allele num: 9768
num of homozygotes: 0

East Asian
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Other
type: Population
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South Asian
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allele frequency: 6.514657980456026e-5
allele num: 15350
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African
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European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5280
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European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.83116645303058e-5
allele num: 54610
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 1.163e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 9.21e-1

BaseQRankSum
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QD
type: SiteQuality
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VQSLOD
type: SiteQuality
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ClippingRankSum
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MQRankSum
type: SiteQuality
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MQ
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DP
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InbreedingCoeff
type: SiteQuality
SIO_000300: -4.6e-3

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

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6942
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 2
allele frequency: 3.654570039834813e-5
allele num: 54726
num of homozygotes: 0

Latino
type: Population
allele count: 1
allele frequency: 1.020408163265306e-4
allele num: 9800
num of homozygotes: 0

African
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allele frequency: 0.0e0
allele num: 7456
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5282
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 15372
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 718
num of homozygotes: 0

ClippingRankSum
type: SiteQuality
SIO_000300: -2.64e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -1.376e0

DP
type: SiteQuality
SIO_000300: 1.077551e6

FS
type: SiteQuality
SIO_000300: 1.016e0

VQSLOD
type: SiteQuality
SIO_000300: 1.59e0

QD
type: SiteQuality
SIO_000300: 1.128e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -4.4e-3

ReadPosRankSum
type: SiteQuality
SIO_000300: 3.18e-1

MQRankSum
type: SiteQuality
SIO_000300: -4.61e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

GenotypeQuality
all individuals: 1294
bin: 4.25e1
variant carriers: 0

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

GenotypeQuality
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bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1767
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3901
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 24372
bin: 6.25e1
variant carriers: 1

GenotypeQuality
all individuals: 1718
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 1719
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 197
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 724
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 333
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 64
bin: 8.25e1
variant carriers: 0

European (Non-Finnish)
type: Population
allele count: 2
allele frequency: 3.65123411713159e-5
allele num: 54776
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 724
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 6.509569066527795e-5
allele num: 15362
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7452
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 1
allele frequency: 1.88465887674331e-4
allele num: 5306
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9804
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6916
num of homozygotes: 0

ClippingRankSum
type: SiteQuality
SIO_000300: -4.62e-1

QD
type: SiteQuality
SIO_000300: 7.34e0

MQRankSum
type: SiteQuality
SIO_000300: 3.22e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -4.4e-3

DP
type: SiteQuality
SIO_000300: 1.083863e6

BaseQRankSum
type: SiteQuality
SIO_000300: 6.38e-1

FS
type: SiteQuality
SIO_000300: 0.0e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

VQSLOD
type: SiteQuality
SIO_000300: 1.33e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 3.1e-2

GenotypeQuality
all individuals: 1034
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2644
bin: 3.75e1
variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 2645
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 377
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 192
bin: 2.5e0
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GenotypeQuality
all individuals: 4033
bin: 3.25e1
variant carriers: 1

GenotypeQuality
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bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1526
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GenotypeQuality
all individuals: 17
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 68
bin: 9.75e1
variant carriers: 28

GenotypeQuality
all individuals: 224
bin: 7.75e1
variant carriers: 1

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7572
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5466
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 16
allele frequency: 2.880599164626242e-4
allele num: 55544
num of homozygotes: 0

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

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 15470
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 732
num of homozygotes: 0

East Asian
type: Population
allele count: 16
allele frequency: 2.258610954263128e-3
allele num: 7084
num of homozygotes: 0

ClippingRankSum
type: SiteQuality
SIO_000300: -1.68e-1

QD
type: SiteQuality
SIO_000300: 1.202e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -3.7e-3

MQRankSum
type: SiteQuality
SIO_000300: 2.01e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -1.898e0

VQSLOD
type: SiteQuality
SIO_000300: 3.56e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

FS
type: SiteQuality
SIO_000300: 1.479e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.31e-1

DP
type: SiteQuality
SIO_000300: 1.120761e6

GenotypeQuality
all individuals: 269
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 73
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 3156
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 277
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3650
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 52
bin: 9.75e1
variant carriers: 12

GenotypeQuality
all individuals: 163
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variant carriers: 0

GenotypeQuality
all individuals: 899
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variant carriers: 0

GenotypeQuality
all individuals: 228
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GenotypeQuality
all individuals: 31164
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variant carriers: 1

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

GenotypeQuality
all individuals: 2793
bin: 6.75e1
variant carriers: 0

European (Non-Finnish)
type: Population
allele count: 9
allele frequency: 1.611632404555547e-4
allele num: 55844
num of homozygotes: 0

East Asian
type: Population
allele count: 1
allele frequency: 1.404099971918001e-4
allele num: 7122
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 1.310272536687631e-4
allele num: 7632
num of homozygotes: 0

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

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10044
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5498
num of homozygotes: 0

South Asian
type: Population
allele count: 2
allele frequency: 1.289989680082559e-4
allele num: 15504
num of homozygotes: 0

MQ
type: SiteQuality
SIO_000300: 6.0e1

FS
type: SiteQuality
SIO_000300: 6.411e0

MQRankSum
type: SiteQuality
SIO_000300: 1.16e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 5.36e-1

DP
type: SiteQuality
SIO_000300: 1.13859e6

InbreedingCoeff
type: SiteQuality
SIO_000300: -3.0e-3

BaseQRankSum
type: SiteQuality
SIO_000300: 1.74e0

ClippingRankSum
type: SiteQuality
SIO_000300: -2.35e-1

VQSLOD
type: SiteQuality
SIO_000300: 8.28e-1

QD
type: SiteQuality
SIO_000300: 1.317e1

GenotypeQuality
all individuals: 253
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 179
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 3073
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variant carriers: 0

GenotypeQuality
all individuals: 210
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variant carriers: 0

GenotypeQuality
all individuals: 749
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variant carriers: 0

GenotypeQuality
all individuals: 2714
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variant carriers: 0

GenotypeQuality
all individuals: 1285
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GenotypeQuality
all individuals: 46
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variant carriers: 4

GenotypeQuality
all individuals: 21
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variant carriers: 0

GenotypeQuality
all individuals: 17
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variant carriers: 0

GenotypeQuality
all individuals: 497
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variant carriers: 0

GenotypeQuality
all individuals: 251
bin: 7.75e1
variant carriers: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5570
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 2
allele frequency: 3.554544485124232e-5
allele num: 56266
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 1.301066874837367e-4
allele num: 7686
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7202
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 15588
num of homozygotes: 0

Latino
type: Population
allele count: 1
allele frequency: 9.885330170027679e-5
allele num: 10116
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 752
num of homozygotes: 0

ReadPosRankSum
type: SiteQuality
SIO_000300: 3.53e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

QD
type: SiteQuality
SIO_000300: 1.296e1

FS
type: SiteQuality
SIO_000300: 7.927e0

MQRankSum
type: SiteQuality
SIO_000300: 2.31e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 3.61e-1

DP
type: SiteQuality
SIO_000300: 1.165056e6

BaseQRankSum
type: SiteQuality
SIO_000300: 1.64e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -3.4e-3

VQSLOD
type: SiteQuality
SIO_000300: 5.74e-1

GenotypeQuality
all individuals: 9706
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2331
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 267
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variant carriers: 0

GenotypeQuality
all individuals: 196
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variant carriers: 0

GenotypeQuality
all individuals: 47
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variant carriers: 5

GenotypeQuality
all individuals: 601
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GenotypeQuality
all individuals: 19
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GenotypeQuality
all individuals: 36120
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GenotypeQuality
all individuals: 2525
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GenotypeQuality
all individuals: 22
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GenotypeQuality
all individuals: 460
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variant carriers: 0

GenotypeQuality
all individuals: 1443
bin: 3.75e1
variant carriers: 0

Latino
type: Population
allele count: 2
allele frequency: 1.957713390759593e-4
allele num: 10216
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5660
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7308
num of homozygotes: 0

African
type: Population
allele count: 3
allele frequency: 3.871966959215281e-4
allele num: 7748
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 15640
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 56856
num of homozygotes: 0

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

ClippingRankSum
type: SiteQuality
SIO_000300: 4.21e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.2e-3

FS
type: SiteQuality
SIO_000300: 6.379e0

VQSLOD
type: SiteQuality
SIO_000300: 1.54e0

BaseQRankSum
type: SiteQuality
SIO_000300: -2.469e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.09e0

MQRankSum
type: SiteQuality
SIO_000300: 7.0e-1

DP
type: SiteQuality
SIO_000300: 1.19019e6

MQ
type: SiteQuality
SIO_000300: 6.0e1

QD
type: SiteQuality
SIO_000300: 1.176e1

GenotypeQuality
all individuals: 100
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 24
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variant carriers: 0

GenotypeQuality
all individuals: 7438
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variant carriers: 0

GenotypeQuality
all individuals: 168
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GenotypeQuality
all individuals: 618
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GenotypeQuality
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GenotypeQuality
all individuals: 1722
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GenotypeQuality
all individuals: 1061
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GenotypeQuality
all individuals: 525
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GenotypeQuality
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GenotypeQuality
all individuals: 622
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variant carriers: 0

GenotypeQuality
all individuals: 51
bin: 9.75e1
variant carriers: 12

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7872
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 764
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5838
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 2
allele frequency: 3.43112026076514e-5
allele num: 58290
num of homozygotes: 0

East Asian
type: Population
allele count: 7
allele frequency: 9.234828496042216e-4
allele num: 7580
num of homozygotes: 0

Latino
type: Population
allele count: 2
allele frequency: 1.898253606681853e-4
allele num: 10536
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 6.3403499873193e-5
allele num: 15772
num of homozygotes: 0

BaseQRankSum
type: SiteQuality
SIO_000300: 1.99e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.6e-3

FS
type: SiteQuality
SIO_000300: 1.2683e1

QD
type: SiteQuality
SIO_000300: 9.77e0

MQRankSum
type: SiteQuality
SIO_000300: 6.4e-2

DP
type: SiteQuality
SIO_000300: 1.246106e6

ReadPosRankSum
type: SiteQuality
SIO_000300: -4.56e-1

VQSLOD
type: SiteQuality
SIO_000300: -1.856e0

ClippingRankSum
type: SiteQuality
SIO_000300: 4.65e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

GenotypeQuality
all individuals: 346
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 41
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 263
bin: 5.75e1
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GenotypeQuality
all individuals: 3860
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GenotypeQuality
all individuals: 124
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
all individuals: 811
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 453
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GenotypeQuality
all individuals: 26
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GenotypeQuality
all individuals: 167
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 451
bin: 5.25e1
variant carriers: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8042
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5924
num of homozygotes: 0

Latino
type: Population
allele count: 1
allele frequency: 9.351037965214139e-5
allele num: 10694
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.68168976187273e-5
allele num: 59464
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 790
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7724
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 15878
num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: 3.2e-2

FS
type: SiteQuality
SIO_000300: 1.0041e1

MQ
type: SiteQuality
SIO_000300: 6.0e1

ClippingRankSum
type: SiteQuality
SIO_000300: -2.54e-1

QD
type: SiteQuality
SIO_000300: 1.645e1

BaseQRankSum
type: SiteQuality
SIO_000300: -1.42e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.4e-3

DP
type: SiteQuality
SIO_000300: 1.277351e6

ReadPosRankSum
type: SiteQuality
SIO_000300: 2.54e-1

MQRankSum
type: SiteQuality
SIO_000300: 7.61e-1

GenotypeQuality
all individuals: 642
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variant carriers: 0

GenotypeQuality
all individuals: 71
bin: 9.75e1
variant carriers: 31

GenotypeQuality
all individuals: 44001
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GenotypeQuality
all individuals: 291
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GenotypeQuality
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GenotypeQuality
all individuals: 5476
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GenotypeQuality
all individuals: 165
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GenotypeQuality
all individuals: 101
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GenotypeQuality
all individuals: 24
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GenotypeQuality
all individuals: 4092
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GenotypeQuality
all individuals: 38
bin: 8.75e1
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GenotypeQuality
all individuals: 370
bin: 4.75e1
variant carriers: 0

Latino
type: Population
allele count: 2
allele frequency: 1.846722068328716e-4
allele num: 10830
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7894
num of homozygotes: 0

South Asian
type: Population
allele count: 10
allele frequency: 6.265664160401002e-4
allele num: 15960
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8232
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 19
allele frequency: 3.148718968545955e-4
allele num: 60342
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6036
num of homozygotes: 0

Other
type: Population
allele count: 1
allele frequency: 1.25e-3
allele num: 800
num of homozygotes: 0

ClippingRankSum
type: SiteQuality
SIO_000300: -5.36e-1

VQSLOD
type: SiteQuality
SIO_000300: 9.429999999999999e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 9.53e-1

QD
type: SiteQuality
SIO_000300: 1.424e1

BaseQRankSum
type: SiteQuality
SIO_000300: 7.7e-2

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.4e-3

MQRankSum
type: SiteQuality
SIO_000300: 1.53e-1

DP
type: SiteQuality
SIO_000300: 1.305505e6

FS
type: SiteQuality
SIO_000300: 2.02e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

GenotypeQuality
all individuals: 116
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 419
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variant carriers: 0

GenotypeQuality
all individuals: 658
bin: 2.75e1
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GenotypeQuality
all individuals: 218
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GenotypeQuality
all individuals: 31
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GenotypeQuality
all individuals: 636
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GenotypeQuality
all individuals: 114
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GenotypeQuality
all individuals: 199
bin: 4.25e1
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GenotypeQuality
all individuals: 275
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GenotypeQuality
all individuals: 408
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GenotypeQuality
all individuals: 41
bin: 9.75e1
variant carriers: 2

GenotypeQuality
all individuals: 23
bin: 9.25e1
variant carriers: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11048
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 61566
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 812
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8470
num of homozygotes: 0

South Asian
type: Population
allele count: 2
allele frequency: 1.242699142537592e-4
allele num: 16094
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6178
num of homozygotes: 0

East Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 8164
num of homozygotes: 0

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.4e-3

MQRankSum
type: SiteQuality
SIO_000300: 1.92e0

ClippingRankSum
type: SiteQuality
SIO_000300: -1.02e-1

FS
type: SiteQuality
SIO_000300: 2.734e0

DP
type: SiteQuality
SIO_000300: 1.341447e6

BaseQRankSum
type: SiteQuality
SIO_000300: -3.686e0

VQSLOD
type: SiteQuality
SIO_000300: -3.541e-1

MQ
type: SiteQuality
SIO_000300: 5.964e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.93e0

QD
type: SiteQuality
SIO_000300: 1.236e1

GenotypeQuality
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bin: 3.75e1
variant carriers: 0

GenotypeQuality
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bin: 1.25e1
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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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: 4.25e1
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 417
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GenotypeQuality
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bin: 9.25e1
variant carriers: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 818
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8564
num of homozygotes: 0

South Asian
type: Population
allele count: 3
allele frequency: 1.857585139318885e-4
allele num: 16150
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11112
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.611811353599175e-5
allele num: 62042
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 1
allele frequency: 1.602050624799744e-4
allele num: 6242
num of homozygotes: 0

East Asian
type: Population
allele count: 1
allele frequency: 1.212709192335678e-4
allele num: 8246
num of homozygotes: 0

DP
type: SiteQuality
SIO_000300: 1.354901e6

ReadPosRankSum
type: SiteQuality
SIO_000300: 7.17e-1

MQRankSum
type: SiteQuality
SIO_000300: -6.2e-2

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.1e-3

VQSLOD
type: SiteQuality
SIO_000300: 1.07e0

BaseQRankSum
type: SiteQuality
SIO_000300: 3.39e0

ClippingRankSum
type: SiteQuality
SIO_000300: -1.69e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

QD
type: SiteQuality
SIO_000300: 1.226e1

FS
type: SiteQuality
SIO_000300: 3.385e0

GenotypeQuality
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variant carriers: 0

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

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 62558
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 826
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8686
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 6.17283950617284e-5
allele num: 16200
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6324
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11170
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8342
num of homozygotes: 0

BaseQRankSum
type: SiteQuality
SIO_000300: -2.179e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.46e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

VQSLOD
type: SiteQuality
SIO_000300: 6.35e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -1.135e0

MQRankSum
type: SiteQuality
SIO_000300: -7.02e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -4.0e-4

FS
type: SiteQuality
SIO_000300: 3.144e0

QD
type: SiteQuality
SIO_000300: 1.317e1

DP
type: SiteQuality
SIO_000300: 1.369326e6

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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variant carriers: 20

GenotypeQuality
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variant carriers: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6370
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8396
num of homozygotes: 0

South Asian
type: Population
allele count: 20
allele frequency: 1.230920728705071e-3
allele num: 16248
num of homozygotes: 0

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

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8756
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 828
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 62820
num of homozygotes: 0

BaseQRankSum
type: SiteQuality
SIO_000300: -2.124e0

ClippingRankSum
type: SiteQuality
SIO_000300: -1.04e-1

MQ
type: SiteQuality
SIO_000300: 5.981e1

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.0e-4

QD
type: SiteQuality
SIO_000300: 1.159e1

DP
type: SiteQuality
SIO_000300: 1.37981e6

FS
type: SiteQuality
SIO_000300: 1.744e0

MQRankSum
type: SiteQuality
SIO_000300: -1.29e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 4.27e-1

VQSLOD
type: SiteQuality
SIO_000300: 2.28e0

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: 683
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variant carriers: 0

European (Non-Finnish)
type: Population
allele count: 2
allele frequency: 3.178033432911714e-5
allele num: 62932
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6426
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8410
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 828
num of homozygotes: 0

Latino
type: Population
allele count: 1
allele frequency: 8.888888888888889e-5
allele num: 11250
num of homozygotes: 0

African
type: Population
allele count: 3
allele frequency: 3.402903811252268e-4
allele num: 8816
num of homozygotes: 0

South Asian
type: Population
allele count: 6
allele frequency: 3.687315634218289e-4
allele num: 16272
num of homozygotes: 0

InbreedingCoeff
type: SiteQuality
SIO_000300: -8.0e-4

VQSLOD
type: SiteQuality
SIO_000300: -1.792e-1

FS
type: SiteQuality
SIO_000300: 1.0298e1

BaseQRankSum
type: SiteQuality
SIO_000300: 2.29e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 5.54e-1

MQRankSum
type: SiteQuality
SIO_000300: 6.6e-2

ClippingRankSum
type: SiteQuality
SIO_000300: -2.51e-1

DP
type: SiteQuality
SIO_000300: 1.385552e6

MQ
type: SiteQuality
SIO_000300: 5.922e1

QD
type: SiteQuality
SIO_000300: 1.284e1

GenotypeQuality
all individuals: 84
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variant carriers: 0

GenotypeQuality
all individuals: 72
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
all individuals: 108
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GenotypeQuality
all individuals: 77
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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: 456
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GenotypeQuality
all individuals: 32
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variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8426
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.586495748191395e-5
allele num: 63032
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11274
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16300
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8862
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6452
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 832
num of homozygotes: 0

ClippingRankSum
type: SiteQuality
SIO_000300: -7.099999999999999e-2

ReadPosRankSum
type: SiteQuality
SIO_000300: 3.32e-1

QD
type: SiteQuality
SIO_000300: 1.149e1

MQRankSum
type: SiteQuality
SIO_000300: 3.08e-1

FS
type: SiteQuality
SIO_000300: 4.316e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.0e-4

VQSLOD
type: SiteQuality
SIO_000300: 1.1e0

BaseQRankSum
type: SiteQuality
SIO_000300: 9.95e-1

MQ
type: SiteQuality
SIO_000300: 5.959e1

DP
type: SiteQuality
SIO_000300: 1.39044e6

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: 136
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variant carriers: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 63132
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 1.12410071942446e-4
allele num: 8896
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8436
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11296
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16306
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6486
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 834
num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: -1.754e0

ClippingRankSum
type: SiteQuality
SIO_000300: 7.199999999999999e-2

FS
type: SiteQuality
SIO_000300: 0.0e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

QD
type: SiteQuality
SIO_000300: 5.15e0

MQRankSum
type: SiteQuality
SIO_000300: -7.199999999999999e-2

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.0e-3

BaseQRankSum
type: SiteQuality
SIO_000300: 5.97e-1

DP
type: SiteQuality
SIO_000300: 1.393257e6

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.25e0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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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: 6.75e1
variant carriers: 0

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

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 836
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.58262906340012e-5
allele num: 63186
num of homozygotes: 0

East Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 8438
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African
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allele count: 0
allele frequency: 0.0e0
allele num: 8912
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South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16328
num of homozygotes: 0

European (Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 6502
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 9.468e0

ClippingRankSum
type: SiteQuality
SIO_000300: 1.95e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 5.97e-1

VQSLOD
type: SiteQuality
SIO_000300: -1.277e-1

DP
type: SiteQuality
SIO_000300: 1.39555e6

QD
type: SiteQuality
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InbreedingCoeff
type: SiteQuality
SIO_000300: -1.2e-3

MQRankSum
type: SiteQuality
SIO_000300: 7.199999999999999e-2

MQ
type: SiteQuality
SIO_000300: 5.959e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 2.3e-2

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

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11318
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 63164
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South Asian
type: Population
allele count: 2
allele frequency: 1.224889759921607e-4
allele num: 16328
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8896
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European (Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 6514
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East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8440
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Other
type: Population
allele count: 0
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allele num: 834
num of homozygotes: 0

QD
type: SiteQuality
SIO_000300: 1.032e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.1e-3

VQSLOD
type: SiteQuality
SIO_000300: 6.37e-1

MQ
type: SiteQuality
SIO_000300: 5.973e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 5.649999999999999e-1

DP
type: SiteQuality
SIO_000300: 1.396607e6

MQRankSum
type: SiteQuality
SIO_000300: 8.34e-1

FS
type: SiteQuality
SIO_000300: 5.975e0

BaseQRankSum
type: SiteQuality
SIO_000300: -1.607e0

ClippingRankSum
type: SiteQuality
SIO_000300: 1.36e-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
all individuals: 123
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GenotypeQuality
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GenotypeQuality
all individuals: 133
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
all individuals: 78
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GenotypeQuality
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variant carriers: 0

East Asian
type: Population
allele count: 3
allele frequency: 3.551977267345489e-4
allele num: 8446
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 7
allele frequency: 1.107139467940404e-4
allele num: 63226
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6530
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Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 840
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Latino
type: Population
allele count: 1
allele frequency: 8.816787162757891e-5
allele num: 11342
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8954
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South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16340
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FS
type: SiteQuality
SIO_000300: 6.27e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: -2.49e-1

MQRankSum
type: SiteQuality
SIO_000300: 3.4e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -3.0e-4

QD
type: SiteQuality
SIO_000300: 1.339e1

DP
type: SiteQuality
SIO_000300: 1.400169e6

VQSLOD
type: SiteQuality
SIO_000300: 8.5e-1

MQ
type: SiteQuality
SIO_000300: 5.943e1

BaseQRankSum
type: SiteQuality
SIO_000300: 1.56e0

ClippingRankSum
type: SiteQuality
SIO_000300: 3.37e-1

GenotypeQuality
all individuals: 85
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 50432
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GenotypeQuality
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bin: 2.5e0
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GenotypeQuality
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bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 101
bin: 5.75e1
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GenotypeQuality
all individuals: 76
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 26
bin: 9.25e1
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GenotypeQuality
all individuals: 32
bin: 8.75e1
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GenotypeQuality
all individuals: 452
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GenotypeQuality
all individuals: 131
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1601
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 131
bin: 2.75e1
variant carriers: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 842
num of homozygotes: 0

Latino
type: Population
allele count: 6
allele frequency: 5.282620179609086e-4
allele num: 11358
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6546
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16342
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8452
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8974
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.581327682722414e-5
allele num: 63238
num of homozygotes: 0

ClippingRankSum
type: SiteQuality
SIO_000300: 3.1e-2

BaseQRankSum
type: SiteQuality
SIO_000300: 1.9e0

VQSLOD
type: SiteQuality
SIO_000300: 1.87e0

MQRankSum
type: SiteQuality
SIO_000300: -3.33e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -5.0e-4

DP
type: SiteQuality
SIO_000300: 1.401184e6

MQ
type: SiteQuality
SIO_000300: 6.0e1

FS
type: SiteQuality
SIO_000300: 3.789e0

QD
type: SiteQuality
SIO_000300: 1.237e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 2.33e-1

GenotypeQuality
all individuals: 112
bin: 2.75e1
variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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variant carriers: 2

GenotypeQuality
all individuals: 130
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GenotypeQuality
all individuals: 71
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GenotypeQuality
all individuals: 455
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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: 4920
bin: 6.75e1
variant carriers: 0

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

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.582378631558959e-5
allele num: 63196
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11376
num of homozygotes: 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: 8456
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 1.11333778668448e-4
allele num: 8982
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 842
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6558
num of homozygotes: 0

MQRankSum
type: SiteQuality
SIO_000300: 8.69e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 4.09e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 5.5e-2

FS
type: SiteQuality
SIO_000300: 2.112e0

ClippingRankSum
type: SiteQuality
SIO_000300: 6.15e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -5.0e-4

QD
type: SiteQuality
SIO_000300: 9.800000000000001e0

DP
type: SiteQuality
SIO_000300: 1.401616e6

VQSLOD
type: SiteQuality
SIO_000300: 5.45e-1

MQ
type: SiteQuality
SIO_000300: 5.97e1

GenotypeQuality
all individuals: 1583
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 58
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 93
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GenotypeQuality
all individuals: 35
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 54
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variant carriers: 15

GenotypeQuality
all individuals: 49
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
all individuals: 50707
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 842
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.582178343142839e-5
allele num: 63204
num of homozygotes: 0

East Asian
type: Population
allele count: 1
allele frequency: 1.182872013248167e-4
allele num: 8454
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6562
num of homozygotes: 0

South Asian
type: Population
allele count: 6
allele frequency: 3.670622782332069e-4
allele num: 16346
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11380
num of homozygotes: 0

African
type: Population
allele count: 7
allele frequency: 7.795100222717149e-4
allele num: 8980
num of homozygotes: 0

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.0e-3

DP
type: SiteQuality
SIO_000300: 1.402626e6

ClippingRankSum
type: SiteQuality
SIO_000300: 1.3e-2

ReadPosRankSum
type: SiteQuality
SIO_000300: -6.4e-2

VQSLOD
type: SiteQuality
SIO_000300: 2.0e0

MQRankSum
type: SiteQuality
SIO_000300: 4.48e-1

FS
type: SiteQuality
SIO_000300: 1.805e0

QD
type: SiteQuality
SIO_000300: 1.18e1

MQ
type: SiteQuality
SIO_000300: 5.974e1

BaseQRankSum
type: SiteQuality
SIO_000300: 1.5e0

GenotypeQuality
all individuals: 105
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 62
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
all individuals: 129
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GenotypeQuality
all individuals: 104
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variant carriers: 0

GenotypeQuality
all individuals: 69
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GenotypeQuality
all individuals: 29
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GenotypeQuality
all individuals: 41
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GenotypeQuality
all individuals: 27
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GenotypeQuality
all individuals: 50715
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variant carriers: 0

GenotypeQuality
all individuals: 710
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GenotypeQuality
all individuals: 1590
bin: 2.25e1
variant carriers: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 842
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11384
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6570
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 2
allele frequency: 3.165458516666139e-5
allele num: 63182
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16338
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8454
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8978
num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: 1.06e0

MQ
type: SiteQuality
SIO_000300: 5.948e1

BaseQRankSum
type: SiteQuality
SIO_000300: -2.805e0

MQRankSum
type: SiteQuality
SIO_000300: 5.13e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 4.46e-1

FS
type: SiteQuality
SIO_000300: 3.773e0

DP
type: SiteQuality
SIO_000300: 1.40161e6

QD
type: SiteQuality
SIO_000300: 1.216e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -7.0e-4

ReadPosRankSum
type: SiteQuality
SIO_000300: 6.33e-1

GenotypeQuality
all individuals: 121
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 29
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variant carriers: 0

GenotypeQuality
all individuals: 27
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GenotypeQuality
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GenotypeQuality
all individuals: 1195
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GenotypeQuality
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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: 50544
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GenotypeQuality
all individuals: 131
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variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8452
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 842
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.585238261310675e-5
allele num: 63082
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11388
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 6.121449559255632e-5
allele num: 16336
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6578
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8932
num of homozygotes: 0

MQRankSum
type: SiteQuality
SIO_000300: 7.3e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 5.649999999999999e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

DP
type: SiteQuality
SIO_000300: 1.399887e6

VQSLOD
type: SiteQuality
SIO_000300: 1.0e0

QD
type: SiteQuality
SIO_000300: 1.184e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 9.13e-1

FS
type: SiteQuality
SIO_000300: 2.965e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -5.999999999999999e-4

BaseQRankSum
type: SiteQuality
SIO_000300: -2.47e0

GenotypeQuality
all individuals: 155
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variant carriers: 0

GenotypeQuality
all individuals: 80
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GenotypeQuality
all individuals: 74
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variant carriers: 0

GenotypeQuality
all individuals: 1284
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
all individuals: 29
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
all individuals: 50410
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GenotypeQuality
all individuals: 40
bin: 9.75e1
variant carriers: 1

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

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8916
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16328
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 62930
num of homozygotes: 0

Latino
type: Population
allele count: 1
allele frequency: 8.781173164734808e-5
allele num: 11388
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 842
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6584
num of homozygotes: 0

MQ
type: SiteQuality
SIO_000300: 6.0e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 2.16e0

FS
type: SiteQuality
SIO_000300: 3.085e0

BaseQRankSum
type: SiteQuality
SIO_000300: -1.012e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -8.0e-4

ClippingRankSum
type: SiteQuality
SIO_000300: -2.397e0

VQSLOD
type: SiteQuality
SIO_000300: -2.536e0

MQRankSum
type: SiteQuality
SIO_000300: -1.5e0

DP
type: SiteQuality
SIO_000300: 1.397835e6

QD
type: SiteQuality
SIO_000300: 6.68e0

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: 26
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GenotypeQuality
all individuals: 718
bin: 7.25e1
variant carriers: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 842
num of homozygotes: 0

Latino
type: Population
allele count: 1
allele frequency: 8.781173164734808e-5
allele num: 11388
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 62910
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8898
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6588
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8446
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16316
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 9.311e0

MQRankSum
type: SiteQuality
SIO_000300: 4.57e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: -2.15e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 1.18e0

QD
type: SiteQuality
SIO_000300: 1.075e1

MQ
type: SiteQuality
SIO_000300: 5.92e1

InbreedingCoeff
type: SiteQuality
SIO_000300: 4.4e-3

BaseQRankSum
type: SiteQuality
SIO_000300: 5.97e-1

VQSLOD
type: SiteQuality
SIO_000300: -9.733000000000001e-1

DP
type: SiteQuality
SIO_000300: 1.396862e6

GenotypeQuality
all individuals: 1340
bin: 7.5e0
variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 63
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GenotypeQuality
all individuals: 14
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GenotypeQuality
all individuals: 36
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GenotypeQuality
all individuals: 42
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GenotypeQuality
all individuals: 1553
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
all individuals: 47
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GenotypeQuality
all individuals: 50453
bin: 6.25e1
variant carriers: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 62910
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6588
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11388
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 1.123848055742864e-4
allele num: 8898
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16316
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 842
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8446
num of homozygotes: 0

ReadPosRankSum
type: SiteQuality
SIO_000300: -2.15e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 4.4e-3

FS
type: SiteQuality
SIO_000300: 9.311e0

MQRankSum
type: SiteQuality
SIO_000300: 4.57e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 5.97e-1

QD
type: SiteQuality
SIO_000300: 1.075e1

DP
type: SiteQuality
SIO_000300: 1.396862e6

MQ
type: SiteQuality
SIO_000300: 5.92e1

VQSLOD
type: SiteQuality
SIO_000300: -9.733000000000001e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 1.18e0