15-42456582-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42456582
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42456582
    reference: chr 15
allele count: 4
allele frequency: 3.296196189597204e-5
allele num: 121352
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.2033G>A
  hgvsp: ENSP00000335193.5:p.Arg678Gln
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.2000G>A
  hgvsp: ENSP00000326534.5:p.Arg667Gln
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561818
  gene symbol: VPS39
  hgvsc: ENST00000561818.1:n.343G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.1494G>A
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 78
  bin: 7.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 118
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 688
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 396
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11739
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 59
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29694
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3133
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1410
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 225
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 30
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 23
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 44
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18
  bin: 9.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 12815
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 27
  bin: 8.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 152
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 41
  bin: 9.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 26
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 14
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 36
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2612
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8750
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2981
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 40949
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2158
  bin: 9.75e1
  variant carriers: 4
genotype quality: GenotypeQuality
  all individuals: 1644
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 15
  bin: 3.25e1
  variant carriers: 0
hgvs: p.Arg667Gln
num of homozygotes: 0
population: European (Finnish)
population: Latino
population: East Asian
population: South Asian
population: African
population: European (Non-Finnish)
population: Other
reference allele: C
site quality: DP
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: MQ
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: FS
site quality: MQRankSum
site quality: BaseQRankSum
site quality: QD

http://identifiers.org/exac.variant/15-42456582-C-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42456582
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42456582
    reference: chr 15
allele count: 1
allele frequency: 8.240490473993011e-6
allele num: 121352
alternate allele: A
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.2000G>T
  hgvsp: ENSP00000326534.5:p.Arg667Leu
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561818
  gene symbol: VPS39
  hgvsc: ENST00000561818.1:n.343G>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.1494G>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.2033G>T
  hgvsp: ENSP00000335193.5:p.Arg678Leu
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 78
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1410
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11739
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 396
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 23
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 152
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 41
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 118
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 30
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 27
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 225
  bin: 5.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 688
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12815
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3133
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29694
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 59
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 44
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 26
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8750
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 40949
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 36
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2981
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2612
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2158
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 1644
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 15
  bin: 3.25e1
  variant carriers: 0
hgvs: p.Arg667Leu
num of homozygotes: 0
population: European (Finnish)
population: East Asian
population: African
population: Other
population: Latino
population: South Asian
population: European (Non-Finnish)
reference allele: C
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: QD
site quality: FS
site quality: MQ
site quality: VQSLOD
site quality: ReadPosRankSum
site quality: DP

15-42456583-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42456583
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42456583
    reference: chr 15
allele count: 3
allele frequency: 2.47222863170386e-5
allele num: 121348
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.2032C>T
  hgvsp: ENSP00000335193.5:p.Arg678Trp
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1999C>T
  hgvsp: ENSP00000326534.5:p.Arg667Trp
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561818
  gene symbol: VPS39
  hgvsc: ENST00000561818.1:n.342C>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.1493C>T
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 151
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29707
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 117
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 687
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 224
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11735
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 25
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 24
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12813
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1410
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 30
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 75
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3136
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 45
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  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 41
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 60
  bin: 7.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 395
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  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 820
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genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
  all individuals: 18
  bin: 4.75e1
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genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
  all individuals: 2610
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genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
  all individuals: 1
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genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
  all individuals: 657
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genotype quality: GenotypeQuality
  all individuals: 0
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  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2980
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genotype quality: GenotypeQuality
  all individuals: 1644
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12
  bin: 3.25e1
  variant carriers: 0
hgvs: p.Arg667Trp
num of homozygotes: 0
population: African
population: South Asian
population: Other
population: European (Non-Finnish)
population: East Asian
population: European (Finnish)
population: Latino
reference allele: G
site quality: MQ
site quality: ClippingRankSum
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: QD
site quality: FS
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: BaseQRankSum
site quality: DP

15-42456591-T-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42456591
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42456591
    reference: chr 15
allele count: 1
allele frequency: 8.239947264337508e-6
allele num: 121360
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561818
  gene symbol: VPS39
  hgvsc: ENST00000561818.1:n.334A>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.1485A>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.2024A>T
  hgvsp: ENSP00000335193.5:p.Asp675Val
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1991A>T
  hgvsp: ENSP00000326534.5:p.Asp664Val
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 75
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 151
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3129
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1408
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 395
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  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29710
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 25
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 224
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12842
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 26
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 34
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 44
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 687
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 117
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  variant carriers: 0
genotype depth: GenotypeDepth
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  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 59
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 41
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 11709
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 654
  bin: 8.75e1
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genotype quality: GenotypeQuality
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  bin: 2.5e0
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genotype quality: GenotypeQuality
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  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2980
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
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  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
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  bin: 7.5e0
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genotype quality: GenotypeQuality
  all individuals: 1
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  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1643
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
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  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 34
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 40981
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
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  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 26
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 14
  bin: 3.25e1
  variant carriers: 0
hgvs: p.Asp664Val
num of homozygotes: 0
population: Latino
population: South Asian
population: African
population: European (Finnish)
population: East Asian
population: Other
population: European (Non-Finnish)
reference allele: T
site quality: VQSLOD
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: MQ
site quality: FS
site quality: DP
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: QD

15-42456594-T-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42456594
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42456594
    reference: chr 15
allele count: 5
allele frequency: 4.120041530018623e-5
allele num: 121358
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.2021A>G
  hgvsp: ENSP00000335193.5:p.Tyr674Cys
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.1482A>G
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561818
  gene symbol: VPS39
  hgvsc: ENST00000561818.1:n.331A>G
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1988A>G
  hgvsp: ENSP00000326534.5:p.Tyr663Cys
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 27
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 25
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 44
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3128
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 224
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1408
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 686
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 75
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12850
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11702
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 34
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 396
  bin: 5.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 60
  bin: 7.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 41
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 116
  bin: 6.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 29709
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 151
  bin: 6.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 41009
  bin: 6.25e1
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genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 36
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 652
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8739
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2596
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2978
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 26
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 4.25e1
  variant carriers: 0
hgvs: p.Tyr663Cys
num of homozygotes: 0
population: African
population: European (Non-Finnish)
population: South Asian
population: European (Finnish)
population: Other
population: Latino
population: East Asian
reference allele: T
site quality: MQRankSum
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: QD
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: ReadPosRankSum
site quality: FS
site quality: DP
site quality: MQ

15-42456596-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42456596
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42456596
    reference: chr 15
allele count: 10
allele frequency: 8.240354664864775e-5
allele num: 121354
alternate allele: A
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1986C>T
  hgvsp: ENST00000318006.5:c.1986C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.1480C>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.2019C>T
  hgvsp: ENST00000348544.4:c.2019C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561818
  gene symbol: VPS39
  hgvsc: ENST00000561818.1:n.329C>T
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 396
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 36
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11700
  bin: 3.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 47
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  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 12858
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3128
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 686
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 40
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29699
  bin: 2.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 12
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 25
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 59
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1406
  bin: 4.25e1
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genotype depth: GenotypeDepth
  all individuals: 75
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 152
  bin: 6.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 115
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 226
  bin: 5.75e1
  variant carriers: 2
genotype quality: GenotypeQuality
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  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
  all individuals: 1639
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
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  bin: 7.25e1
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genotype quality: GenotypeQuality
  all individuals: 38
  bin: 2.25e1
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genotype quality: GenotypeQuality
  all individuals: 2152
  bin: 9.75e1
  variant carriers: 10
genotype quality: GenotypeQuality
  all individuals: 41007
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 18
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 2.75e1
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genotype quality: GenotypeQuality
  all individuals: 651
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genotype quality: GenotypeQuality
  all individuals: 11
  bin: 3.25e1
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genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.25e1
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genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 815
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2976
  bin: 7.75e1
  variant carriers: 0
hgvs: p.Tyr662Tyr
num of homozygotes: 0
population: European (Finnish)
population: South Asian
population: Other
population: Latino
population: African
population: East Asian
population: European (Non-Finnish)
reference allele: G
site quality: BaseQRankSum
site quality: VQSLOD
site quality: MQRankSum
site quality: MQ
site quality: QD
site quality: FS
site quality: ClippingRankSum
site quality: ReadPosRankSum
site quality: InbreedingCoeff
site quality: DP

15-42456599-G-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42456599
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42456599
    reference: chr 15
allele count: 6
allele frequency: 4.944131316127757e-5
allele num: 121356
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.2016C>G
  hgvsp: ENSP00000335193.5:p.Ser672Arg
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561818
  gene symbol: VPS39
  hgvsc: ENST00000561818.1:n.326C>G
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.1477C>G
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1983C>G
  hgvsp: ENSP00000326534.5:p.Ser661Arg
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 39
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 44
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 40
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 395
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  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 28
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 224
  bin: 5.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 77
  bin: 7.25e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 114
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 685
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3123
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12877
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11697
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29694
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 150
  bin: 6.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 59
  bin: 7.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1404
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 25
  bin: 8.75e1
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genotype depth: GenotypeDepth
  all individuals: 17
  bin: 9.25e1
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genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
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  bin: 1.75e1
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genotype quality: GenotypeQuality
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  bin: 7.5e0
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genotype quality: GenotypeQuality
  all individuals: 12
  bin: 3.75e1
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genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
  all individuals: 12
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genotype quality: GenotypeQuality
  all individuals: 2142
  bin: 9.75e1
  variant carriers: 6
genotype quality: GenotypeQuality
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  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8737
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genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
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genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
  all individuals: 9
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genotype quality: GenotypeQuality
  all individuals: 814
  bin: 9.25e1
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genotype quality: GenotypeQuality
  all individuals: 9
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2976
  bin: 7.75e1
  variant carriers: 0
hgvs: p.Ser661Arg
num of homozygotes: 0
population: Latino
population: African
population: European (Finnish)
population: European (Non-Finnish)
population: South Asian
population: East Asian
population: Other
reference allele: G
site quality: ReadPosRankSum
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: DP
site quality: FS
site quality: VQSLOD
site quality: MQ
site quality: QD
site quality: BaseQRankSum

15-42456617-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42456617
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42456617
    reference: chr 15
allele count: 1
allele frequency: 8.241577108195424e-6
allele num: 121336
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.1459G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1998G>A
  hgvsp: ENSP00000335193.5:p.Met666Ile
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1965G>A
  hgvsp: ENSP00000326534.5:p.Met655Ile
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561818
  gene symbol: VPS39
  hgvsc: ENST00000561818.1:n.308G>A
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 12934
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1400
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29669
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 394
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 679
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 147
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 25
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 40
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 113
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 74
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 74
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3103
  bin: 3.75e1
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genotype depth: GenotypeDepth
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  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11641
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  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 223
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 44
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 59
  bin: 7.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 21
  bin: 4.25e1
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genotype quality: GenotypeQuality
  all individuals: 24
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genotype quality: GenotypeQuality
  all individuals: 808
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genotype quality: GenotypeQuality
  all individuals: 643
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genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
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  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2583
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  variant carriers: 0
genotype quality: GenotypeQuality
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  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1626
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genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
  all individuals: 0
  bin: 7.5e0
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genotype quality: GenotypeQuality
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  bin: 2.25e1
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genotype quality: GenotypeQuality
  all individuals: 18
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2942
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 24
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 45
  bin: 5.25e1
  variant carriers: 0
hgvs: p.Met655Ile
num of homozygotes: 0
population: European (Non-Finnish)
population: Other
population: African
population: European (Finnish)
population: East Asian
population: Latino
population: South Asian
reference allele: C
site quality: QD
site quality: BaseQRankSum
site quality: VQSLOD
site quality: MQ
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: FS
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: DP

15-42456620-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42456620
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42456620
    reference: chr 15
allele count: 1
allele frequency: 8.241712957621112e-6
allele num: 121334
alternate allele: A
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1962C>T
  hgvsp: ENST00000318006.5:c.1962C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.1456C>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1995C>T
  hgvsp: ENST00000348544.4:c.1995C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561818
  gene symbol: VPS39
  hgvsc: ENST00000561818.1:n.305C>T
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1399
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 74
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 86
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 41
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 113
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 38
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 223
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29665
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 395
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 44
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 677
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 39
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 58
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3104
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12936
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 147
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 25
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11625
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 807
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 643
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 43
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 22
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 41028
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 69
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 31
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 32
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1625
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8703
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2578
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2939
  bin: 7.75e1
  variant carriers: 0
hgvs: p.Leu654Leu
num of homozygotes: 0
population: Latino
population: East Asian
population: Other
population: African
population: European (Finnish)
population: European (Non-Finnish)
population: South Asian
reference allele: G
site quality: FS
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: QD
site quality: MQ
site quality: ClippingRankSum
site quality: DP
site quality: BaseQRankSum

15-42456633-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42456633
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42456633
    reference: chr 15
allele count: 3
allele frequency: 2.473370049137618e-5
allele num: 121292
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561818
  gene symbol: VPS39
  hgvsc: ENST00000561818.1:n.292G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1949G>A
  hgvsp: ENSP00000326534.5:p.Arg650Gln
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1982G>A
  hgvsp: ENSP00000335193.5:p.Arg661Gln
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.1443G>A
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 13111
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 59
  bin: 7.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 223
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 120
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 25
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 77
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29565
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11515
  bin: 3.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 148
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3071
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 112
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 672
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 392
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 44
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 40
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 53
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 74
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1388
  bin: 4.25e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 8598
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 629
  bin: 8.75e1
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genotype quality: GenotypeQuality
  all individuals: 68
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 39
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
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  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 103
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genotype quality: GenotypeQuality
  all individuals: 2
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 79
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2538
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 31
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 50
  bin: 3.75e1
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genotype quality: GenotypeQuality
  all individuals: 794
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1599
  bin: 8.25e1
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genotype quality: GenotypeQuality
  all individuals: 2100
  bin: 9.75e1
  variant carriers: 3
genotype quality: GenotypeQuality
  all individuals: 41036
  bin: 6.25e1
  variant carriers: 0
hgvs: p.Arg650Gln
num of homozygotes: 0
population: European (Finnish)
population: East Asian
population: Latino
population: European (Non-Finnish)
population: South Asian
population: African
population: Other
reference allele: C
site quality: FS
site quality: MQRankSum
site quality: ClippingRankSum
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: DP
site quality: BaseQRankSum
site quality: MQ
site quality: QD
site quality: ReadPosRankSum

15-42456644-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42456644
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42456644
    reference: chr 15
allele count: 6
allele frequency: 4.948861761794787e-5
allele num: 121240
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1971G>A
  hgvsp: ENST00000348544.4:c.1971G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1938G>A
  hgvsp: ENST00000318006.5:c.1938G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561818
  gene symbol: VPS39
  hgvsc: ENST00000561818.1:n.281G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.1432G>A
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 44
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 668
  bin: 4.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 79
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 147
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11367
  bin: 3.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 73
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 59
  bin: 7.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 223
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 112
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1351
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3044
  bin: 3.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 119
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 125
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13295
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 386
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 26
  bin: 8.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 40
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29531
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 41271
  bin: 6.25e1
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genotype quality: GenotypeQuality
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  bin: 5.75e1
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genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
  all individuals: 8536
  bin: 6.75e1
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genotype quality: GenotypeQuality
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  bin: 4.75e1
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genotype quality: GenotypeQuality
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  bin: 1.25e1
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genotype quality: GenotypeQuality
  all individuals: 3
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genotype quality: GenotypeQuality
  all individuals: 35
  bin: 2.75e1
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genotype quality: GenotypeQuality
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  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2838
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2073
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  variant carriers: 6
genotype quality: GenotypeQuality
  all individuals: 158
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.75e1
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genotype quality: GenotypeQuality
  all individuals: 57
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2504
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  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 54
  bin: 3.75e1
  variant carriers: 0
hgvs: p.Leu646Leu
num of homozygotes: 0
population: European (Finnish)
population: African
population: South Asian
population: European (Non-Finnish)
population: Other
population: East Asian
population: Latino
reference allele: C
site quality: QD
site quality: VQSLOD
site quality: ClippingRankSum
site quality: MQ
site quality: InbreedingCoeff
site quality: FS
site quality: BaseQRankSum
site quality: DP
site quality: ReadPosRankSum
site quality: MQRankSum

15-42456646-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42456646
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42456646
    reference: chr 15
allele count: 1
allele frequency: 8.248919391559706e-6
allele num: 121228
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1969C>T
  hgvsp: ENST00000348544.4:c.1969C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1936C>T
  hgvsp: ENST00000318006.5:c.1936C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.1430C>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561818
  gene symbol: VPS39
  hgvsc: ENST00000561818.1:n.279C>T
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 386
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 137
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 147
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 223
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 44
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13305
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 40
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29525
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1348
  bin: 4.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 112
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 124
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 58
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 89
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 9.25e1
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genotype depth: GenotypeDepth
  all individuals: 3034
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
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  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11357
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 662
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 25
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
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  bin: 3.75e1
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genotype quality: GenotypeQuality
  all individuals: 41
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
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  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
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  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
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  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2838
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
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  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 56
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2496
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 183
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 51
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 615
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 40
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 41307
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 775
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  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8528
  bin: 6.75e1
  variant carriers: 0
hgvs: p.Leu646Leu
num of homozygotes: 0
population: South Asian
population: European (Non-Finnish)
population: African
population: East Asian
population: European (Finnish)
population: Latino
population: Other
reference allele: G
site quality: VQSLOD
site quality: MQ
site quality: MQRankSum
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: QD
site quality: FS
site quality: DP
site quality: BaseQRankSum
site quality: ReadPosRankSum

15-42456652-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42456652
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42456652
    reference: chr 15
allele count: 2
allele frequency: 1.650600818698006e-5
allele num: 121168
alternate allele: T
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1930G>A
  hgvsp: ENSP00000326534.5:p.Gly644Ser
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1963G>A
  hgvsp: ENSP00000335193.5:p.Gly655Ser
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.1424G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561818
  gene symbol: VPS39
  hgvsc: ENST00000561818.1:n.273G>A
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 223
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11298
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1331
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 40
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 119
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 25
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 58
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 44
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13381
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29445
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 136
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3017
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 112
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 387
  bin: 5.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 192
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 147
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 661
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 73
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 159
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2478
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 41177
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 65
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2806
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 91
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8480
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 245
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2055
  bin: 9.75e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 59
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 61
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 65
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 33
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 609
  bin: 8.75e1
  variant carriers: 0
hgvs: p.Gly644Ser
num of homozygotes: 0
population: African
population: European (Finnish)
population: South Asian
population: East Asian
population: European (Non-Finnish)
population: Other
population: Latino
reference allele: C
site quality: BaseQRankSum
site quality: MQ
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: ClippingRankSum
site quality: DP
site quality: FS
site quality: InbreedingCoeff
site quality: QD

15-42456657-T-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42456657
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42456657
    reference: chr 15
allele count: 6
allele frequency: 4.953519475587405e-5
allele num: 121126
alternate allele: C
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1925A>G
  hgvsp: ENSP00000326534.5:p.Glu642Gly
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.1419A>G
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561818
  gene symbol: VPS39
  hgvsc: ENST00000561818.1:n.268A>G
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1958A>G
  hgvsp: ENSP00000335193.5:p.Glu653Gly
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 661
  bin: 4.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 1324
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 73
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 223
  bin: 5.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 112
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29400
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 140
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 385
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 147
  bin: 6.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
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  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 244
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 25
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11210
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3002
  bin: 3.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 13452
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 40
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 58
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 44
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8448
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
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  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 61
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
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  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2795
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 41
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 767
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 41230
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 57
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 92
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  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 298
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1544
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 121
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2445
  bin: 7.25e1
  variant carriers: 0
hgvs: p.Glu642Gly
num of homozygotes: 0
population: Latino
population: African
population: Other
population: European (Non-Finnish)
population: East Asian
population: European (Finnish)
population: South Asian
reference allele: T
site quality: FS
site quality: MQRankSum
site quality: MQ
site quality: BaseQRankSum
site quality: QD
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: DP
site quality: ClippingRankSum

15-42456661-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42456661
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42456661
    reference: chr 15
allele count: 3
allele frequency: 2.477987213585978e-5
allele num: 121066
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.1415G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1954G>A
  hgvsp: ENSP00000335193.5:p.Glu652Lys
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561818
  gene symbol: VPS39
  hgvsc: ENST00000561818.1:n.264G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1921G>A
  hgvsp: ENSP00000326534.5:p.Glu641Lys
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 146
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 655
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13505
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 74
  bin: 7.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 29300
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1321
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 310
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 25
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 385
  bin: 5.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 165
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  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 40
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2990
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 112
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11174
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  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 222
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 164
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 58
  bin: 7.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 1530
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
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  bin: 1.25e1
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genotype quality: GenotypeQuality
  all individuals: 2
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2429
  bin: 7.25e1
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genotype quality: GenotypeQuality
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  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 90
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2042
  bin: 9.75e1
  variant carriers: 3
genotype quality: GenotypeQuality
  all individuals: 94
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
  all individuals: 764
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 606
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
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  bin: 1.75e1
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genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
  all individuals: 2779
  bin: 7.75e1
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genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
  all individuals: 8411
  bin: 6.75e1
  variant carriers: 0
hgvs: p.Glu641Lys
num of homozygotes: 0
population: European (Finnish)
population: European (Non-Finnish)
population: East Asian
population: Other
population: African
population: South Asian
population: Latino
reference allele: C
site quality: VQSLOD
site quality: FS
site quality: QD
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: DP
site quality: ReadPosRankSum
site quality: MQ
site quality: BaseQRankSum

15-42456662-T-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42456662
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42456662
    reference: chr 15
allele count: 3
allele frequency: 2.478560452089426e-5
allele num: 121038
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.1414A>G
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1920A>G
  hgvsp: ENST00000318006.5:c.1920A>G(p.%3D)
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1953A>G
  hgvsp: ENST00000348544.4:c.1953A>G(p.%3D)
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561818
  gene symbol: VPS39
  hgvsc: ENST00000561818.1:n.263A>G
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1321
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 654
  bin: 4.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 181
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11145
  bin: 3.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
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  variant carriers: 0
genotype depth: GenotypeDepth
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genotype depth: GenotypeDepth
  all individuals: 43
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 326
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  variant carriers: 0
genotype depth: GenotypeDepth
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  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29292
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 57
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 112
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 73
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 170
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 146
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 384
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  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 40
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 222
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2989
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
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  variant carriers: 0
genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
  all individuals: 41160
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genotype quality: GenotypeQuality
  all individuals: 92
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
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  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2425
  bin: 7.25e1
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genotype quality: GenotypeQuality
  all individuals: 95
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 385
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
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  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8407
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1522
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 69
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 151
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 761
  bin: 9.25e1
  variant carriers: 0
hgvs: p.Gly640Gly
num of homozygotes: 0
population: Latino
population: European (Finnish)
population: South Asian
population: European (Non-Finnish)
population: African
population: East Asian
population: Other
reference allele: T
site quality: QD
site quality: InbreedingCoeff
site quality: FS
site quality: MQRankSum
site quality: ClippingRankSum
site quality: MQ
site quality: ReadPosRankSum
site quality: BaseQRankSum
site quality: DP
site quality: VQSLOD

http://identifiers.org/exac.variant/15-42456663-C-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42456663
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42456663
    reference: chr 15
allele count: 10
allele frequency: 8.263643275047102e-5
allele num: 121012
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561818
  gene symbol: VPS39
  hgvsc: ENST00000561818.1:n.262G>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1919G>T
  hgvsp: ENSP00000326534.5:p.Gly640Val
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1952G>T
  hgvsp: ENSP00000335193.5:p.Gly651Val
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.1413G>T
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 195
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11133
  bin: 3.25e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 172
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 222
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 111
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 352
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 57
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 26
  bin: 8.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13525
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2989
  bin: 3.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 29245
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 385
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 655
  bin: 4.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 1319
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 146
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 73
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 41
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 74
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 104
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 125
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2415
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 100
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 167
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 412
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 41102
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 605
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2045
  bin: 9.75e1
  variant carriers: 10
genotype quality: GenotypeQuality
  all individuals: 39
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2762
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 77
  bin: 3.75e1
  variant carriers: 0
hgvs: p.Gly640Val
num of homozygotes: 0
population: Other
population: African
population: European (Finnish)
population: East Asian
population: European (Non-Finnish)
population: Latino
population: South Asian
reference allele: C
site quality: FS
site quality: MQRankSum
site quality: ClippingRankSum
site quality: MQ
site quality: ReadPosRankSum
site quality: BaseQRankSum
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: DP
site quality: QD

15-42456666-G-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42456666
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42456666
    reference: chr 15
allele count: 10
allele frequency: 8.26856292376385e-5
allele num: 120940
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561818
  gene symbol: VPS39
  hgvsc: ENST00000561818.1:n.259C>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1949C>A
  hgvsp: ENSP00000335193.5:p.Ala650Asp
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1916C>A
  hgvsp: ENSP00000326534.5:p.Ala639Asp
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.1410C>A
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 57
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 223
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 203
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1315
  bin: 4.25e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 146
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29147
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 25
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 431
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13551
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 228
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11085
  bin: 3.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 111
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 386
  bin: 5.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 73
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 652
  bin: 4.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2972
  bin: 3.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 41
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 93
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 753
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 599
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1506
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 119
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 109
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2039
  bin: 9.75e1
  variant carriers: 10
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 92
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 181
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 503
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2736
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8362
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 152
  bin: 5.75e1
  variant carriers: 0
hgvs: p.Ala639Asp
num of homozygotes: 0
population: European (Finnish)
population: South Asian
population: Latino
population: East Asian
population: African
population: European (Non-Finnish)
population: Other
reference allele: G
site quality: InbreedingCoeff
site quality: FS
site quality: BaseQRankSum
site quality: MQ
site quality: ClippingRankSum
site quality: MQRankSum
site quality: VQSLOD
site quality: QD
site quality: DP
site quality: ReadPosRankSum

15-42456671-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42456671
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42456671
    reference: chr 15
allele count: 1
allele frequency: 8.275131574592036e-6
allele num: 120844
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1944C>T
  hgvsp: ENST00000348544.4:c.1944C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.1405C>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1911C>T
  hgvsp: ENST00000318006.5:c.1911C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561818
  gene symbol: VPS39
  hgvsc: ENST00000561818.1:n.254C>T
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 13652
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10957
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1301
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 540
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 278
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 146
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 222
  bin: 5.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 25
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 383
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29063
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 218
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 73
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 40
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 57
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 647
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2933
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 111
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 139
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 41100
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
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  bin: 4.75e1
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genotype quality: GenotypeQuality
  all individuals: 618
  bin: 2.25e1
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genotype quality: GenotypeQuality
  all individuals: 3
  bin: 2.5e0
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genotype quality: GenotypeQuality
  all individuals: 748
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 112
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2370
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2691
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genotype quality: GenotypeQuality
  all individuals: 48
  bin: 4.25e1
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genotype quality: GenotypeQuality
  all individuals: 156
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 151
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 93
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2019
  bin: 9.75e1
  variant carriers: 1
hgvs: p.Val637Val
num of homozygotes: 0
population: South Asian
population: European (Non-Finnish)
population: African
population: Latino
population: European (Finnish)
population: East Asian
population: Other
reference allele: G
site quality: FS
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: MQ
site quality: VQSLOD
site quality: ClippingRankSum
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: QD
site quality: DP

15-42456675-G-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42456675
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42456675
    reference: chr 15
allele count: 1
allele frequency: 8.281573498964803e-6
allele num: 120750
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1940C>G
  hgvsp: ENSP00000335193.5:p.Pro647Arg
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561818
  gene symbol: VPS39
  hgvsc: ENST00000561818.1:n.250C>G
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1907C>G
  hgvsp: ENSP00000326534.5:p.Pro636Arg
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.1401C>G
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 57
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 274
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1298
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 322
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13628
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 25
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10875
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 146
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 383
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2923
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 111
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 699
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 648
  bin: 4.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 28922
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 73
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 40
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 221
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 40935
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 747
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 584
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  variant carriers: 0
genotype quality: GenotypeQuality
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  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 101
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 195
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2011
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 2654
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8242
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 179
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 151
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 758
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 140
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 1.75e1
  variant carriers: 0
hgvs: p.Pro636Arg
num of homozygotes: 0
population: Other
population: South Asian
population: African
population: East Asian
population: European (Non-Finnish)
population: Latino
population: European (Finnish)
reference allele: G
site quality: QD
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: VQSLOD
site quality: ReadPosRankSum
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: DP
site quality: MQ
site quality: FS

15-42456687-T-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42456687
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42456687
    reference: chr 15
allele count: 1
allele frequency: 8.31282835672009e-6
allele num: 120296
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1931-3A>C
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561818
  gene symbol: VPS39
  hgvsc: ENST00000561818.1:n.238A>C
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.1389A>C
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1898-3A>C
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: splice region
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 13550
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 28280
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 57
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10420
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 221
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 539
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 513
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 379
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1260
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1597
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 145
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2789
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 73
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 112
  bin: 6.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 25
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 641
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 40
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 430
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1524
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2489
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1986
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 2178
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 105
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 146
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 365
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7955
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 248
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 236
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 710
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1382
  bin: 8.25e1
  variant carriers: 0
hgvs: c.1898-3A>C
num of homozygotes: 0
population: East Asian
population: Other
population: European (Finnish)
population: African
population: European (Non-Finnish)
population: South Asian
population: Latino
reference allele: T
site quality: MQRankSum
site quality: FS
site quality: InbreedingCoeff
site quality: MQ
site quality: BaseQRankSum
site quality: VQSLOD
site quality: DP
site quality: QD
site quality: ClippingRankSum
site quality: ReadPosRankSum

15-42456697-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42456697
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42456697
    reference: chr 15
allele count: 5
allele frequency: 4.172926055750292e-5
allele num: 119820
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1931-13G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1898-13G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.1379G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561818
  gene symbol: VPS39
  hgvsc: ENST00000561818.1:n.228G>A
  variant of: http://identifiers.org/hgnc/20593
canonical: false
consequence: non coding transcript exon
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1243
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2712
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 25
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9914
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3054
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 111
  bin: 6.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 26941
  bin: 2.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 145
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 220
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 40
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 759
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 379
  bin: 5.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1027
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 57
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13294
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 641
  bin: 4.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 73
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 544
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 16
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 710
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1318
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7342
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 184
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 157
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 898
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 17
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 699
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 466
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2579
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1979
  bin: 9.75e1
  variant carriers: 5
genotype quality: GenotypeQuality
  all individuals: 326
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2037
  bin: 7.25e1
  variant carriers: 0
num of homozygotes: 0
population: African
population: East Asian
population: Other
population: Latino
population: European (Finnish)
population: South Asian
population: European (Non-Finnish)
reference allele: C
site quality: MQRankSum
site quality: ClippingRankSum
site quality: DP
site quality: BaseQRankSum
site quality: QD
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: FS
site quality: MQ
site quality: ReadPosRankSum

15-42456699-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42456699
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42456699
    reference: chr 15
allele count: 3
allele frequency: 2.505177366557552e-5
allele num: 119752
alternate allele: G
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1898-15T>C
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.1377T>C
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561818
  gene symbol: VPS39
  hgvsc: ENST00000561818.1:n.226T>C
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1931-15T>C
  variant of: http://identifiers.org/hgnc/20593
canonical: false
consequence: non coding transcript exon
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 57
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 220
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 73
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 795
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 378
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9776
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 145
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3475
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1238
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 26603
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2691
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1223
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 40
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 25
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13145
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 111
  bin: 6.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 639
  bin: 4.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1302
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1062
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 817
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 545
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2839
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2328
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1972
  bin: 9.75e1
  variant carriers: 3
genotype quality: GenotypeQuality
  all individuals: 197
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 162
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2002
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
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  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 38313
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 16
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 303
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7258
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 328
  bin: 5.75e1
  variant carriers: 0
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: A
site quality: FS
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: VQSLOD
site quality: ClippingRankSum
site quality: MQ
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: QD
site quality: DP

15-42456702-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42456702
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42456702
    reference: chr 15
allele count: 2
allele frequency: 1.672996168838773e-5
allele num: 119546
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.1374G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561818
  gene symbol: VPS39
  hgvsc: ENST00000561818.1:n.223G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1898-18G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1931-18G>A
  variant of: http://identifiers.org/hgnc/20593
canonical: false
consequence: non coding transcript exon
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 2673
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 638
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9563
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1677
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 110
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 25924
  bin: 2.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 221
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 25
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 145
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 867
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 57
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4244
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12755
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 40
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1236
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 73
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 378
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 28
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 376
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  variant carriers: 1
genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
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  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 37187
  bin: 6.25e1
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genotype quality: GenotypeQuality
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  bin: 6.75e1
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genotype quality: GenotypeQuality
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  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1032
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 310
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 762
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 252
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
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  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3328
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 528
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 224
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2250
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1416
  bin: 3.25e1
  variant carriers: 0
num of homozygotes: 0
population: European (Finnish)
population: European (Non-Finnish)
population: Latino
population: South Asian
population: Other
population: East Asian
population: African
reference allele: C
site quality: MQ
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: BaseQRankSum
site quality: MQRankSum
site quality: QD
site quality: FS
site quality: ClippingRankSum
site quality: DP
site quality: ReadPosRankSum

http://identifiers.org/exac.variant/15-42456704-C-CA
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42456704
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42456705
    reference: chr 15
allele count: 1
allele frequency: 8.369181326682624e-6
allele num: 119486
alternate allele: CA
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.1371dupT
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561818
  gene symbol: VPS39
  hgvsc: ENST00000561818.1:n.220dupT
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1898-21dupT
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1931-21dupT
  variant of: http://identifiers.org/hgnc/20593
canonical: false
consequence: non coding transcript exon
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 74
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1222
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 57
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 905
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 109
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 378
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2027
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 145
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 220
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 637
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 23
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4809
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9381
  bin: 3.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 12525
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 25410
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 40
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 25
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2659
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 522
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2193
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 36
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7002
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1891
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1235
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3713
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1666
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 371
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 681
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 351
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 281
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 23
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 261
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1156
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 14
  bin: 1.25e1
  variant carriers: 0
num of homozygotes: 0
population: East Asian
population: African
population: European (Finnish)
population: South Asian
population: European (Non-Finnish)
population: Other
population: Latino
reference allele: C
site quality: MQ
site quality: ClippingRankSum
site quality: FS
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: QD
site quality: VQSLOD
site quality: DP
site quality: BaseQRankSum
site quality: InbreedingCoeff

15-42456704-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42456704
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42456704
    reference: chr 15
allele count: 2
allele frequency: 1.673836265336525e-5
allele num: 119486
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561818
  gene symbol: VPS39
  hgvsc: ENST00000561818.1:n.221G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1898-20G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.1372G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1931-20G>A
  variant of: http://identifiers.org/hgnc/20593
canonical: false
consequence: non coding transcript exon
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 40
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 378
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 25410
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2027
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 109
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 57
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 23
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 25
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12525
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 637
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4809
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1222
  bin: 4.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 905
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9381
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 220
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2659
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 74
  bin: 7.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 145
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2193
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 261
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1235
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 36436
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1666
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 351
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1156
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 14
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 281
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 36
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 681
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 23
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 902
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1891
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 522
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 371
  bin: 5.75e1
  variant carriers: 0
num of homozygotes: 0
population: Other
population: African
population: European (Finnish)
population: Latino
population: South Asian
population: East Asian
population: European (Non-Finnish)
reference allele: C
site quality: ReadPosRankSum
site quality: FS
site quality: BaseQRankSum
site quality: MQ
site quality: MQRankSum
site quality: DP
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: QD

15-42456734-GT-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42456734
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42456733
    reference: chr 15
allele count: 1
allele frequency: 8.595348197555483e-6
allele num: 116342
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1931-51delA
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.1341delA
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561818
  gene symbol: VPS39
  hgvsc: ENST00000561818.1:n.190delA
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1898-51delA
  variant of: http://identifiers.org/hgnc/20593
canonical: false
consequence: non coding transcript exon
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1875
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14927
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 626
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 377
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2325
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 57
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 73
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 220
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 108
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15536
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 9470
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8743
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 40
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 25
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4811
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1178
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 145
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 109
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6370
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 78
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 439
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1256
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 842
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7224
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5788
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3687
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 404
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 359
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3490
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7927
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3959
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 642
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 486
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1033
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9751
  bin: 6.25e1
  variant carriers: 0
num of homozygotes: 0
population: East Asian
population: Latino
population: European (Finnish)
population: South Asian
population: European (Non-Finnish)
population: Other
population: African
reference allele: GT
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: QD
site quality: MQ
site quality: DP
site quality: MQRankSum
site quality: BaseQRankSum
site quality: FS
site quality: ClippingRankSum
site quality: ReadPosRankSum

15-42457143-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457143
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457143
    reference: chr 15
allele count: 1
allele frequency: 8.279242283746192e-6
allele num: 120784
alternate allele: A
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1897+51C>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.933C>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.482+51C>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.205C>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1930+51C>T
  variant of: http://identifiers.org/hgnc/20593
canonical: false
consequence: non coding transcript exon
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 7358
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 706
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1237
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9445
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10908
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 248
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5156
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 535
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2891
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 586
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 217
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2654
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9981
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 4487
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1116
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 389
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 321
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1643
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 822
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 18
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 18
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3122
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4951
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4733
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 534
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 17
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1078
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 65
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8359
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 421
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 690
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1221
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 628
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 525
  bin: 4.25e1
  variant carriers: 0
num of homozygotes: 0
population: Latino
population: East Asian
population: African
population: South Asian
population: European (Non-Finnish)
population: European (Finnish)
population: Other
reference allele: G
site quality: BaseQRankSum
site quality: MQ
site quality: FS
site quality: DP
site quality: ReadPosRankSum
site quality: QD
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: VQSLOD
site quality: MQRankSum

15-42457160-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457160
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457160
    reference: chr 15
allele count: 1
allele frequency: 8.270204108637402e-6
allele num: 120916
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.188G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1897+34G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.916G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1930+34G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.482+34G>A
  variant of: http://identifiers.org/hgnc/20593
canonical: false
consequence: non coding transcript exon
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 822
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 586
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 707
  bin: 7.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 221
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9998
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1642
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4495
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 859
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6758
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1116
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7360
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11117
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9931
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 973
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 389
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 535
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 217
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 321
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2656
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 205
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 387
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11292
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 14
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 329
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 439
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4723
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21700
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 283
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 16
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 454
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4907
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 253
  bin: 4.25e1
  variant carriers: 0
num of homozygotes: 0
population: East Asian
population: African
population: Latino
population: European (Non-Finnish)
population: South Asian
population: Other
population: European (Finnish)
reference allele: C
site quality: VQSLOD
site quality: MQ
site quality: MQRankSum
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: DP
site quality: InbreedingCoeff
site quality: FS
site quality: QD
site quality: ReadPosRankSum

15-42457161-T-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457161
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457161
    reference: chr 15
allele count: 1
allele frequency: 8.270067318347971e-6
allele num: 120918
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.187A>G
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.482+33A>G
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1897+33A>G
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1930+33A>G
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.915A>G
  variant of: http://identifiers.org/hgnc/20593
canonical: false
consequence: non coding transcript exon
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 10004
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 823
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 748
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 221
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 706
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1116
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1642
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4494
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9958
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2657
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 535
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7360
  bin: 4.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 6879
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11157
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 891
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 389
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 321
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 586
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 217
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 231
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 404
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4720
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 85
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4110
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3160
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 16
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 261
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 423
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 269
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2654
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21699
  bin: 9.75e1
  variant carriers: 1
num of homozygotes: 0
population: East Asian
population: South Asian
population: European (Finnish)
population: Latino
population: African
population: European (Non-Finnish)
population: Other
reference allele: T
site quality: ReadPosRankSum
site quality: DP
site quality: BaseQRankSum
site quality: MQRankSum
site quality: MQ
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: FS
site quality: QD
site quality: ClippingRankSum

15-42457167-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457167
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457167
    reference: chr 15
allele count: 1
allele frequency: 8.266922390132602e-6
allele num: 120964
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.181G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1930+27G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.909G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.482+27G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1897+27G>A
  variant of: http://identifiers.org/hgnc/20593
canonical: false
consequence: non coding transcript exon
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4494
  bin: 4.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1116
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 586
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 321
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1642
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2656
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 514
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 217
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10019
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7368
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11293
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 823
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 199
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 685
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 535
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 389
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 706
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10183
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6959
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 283
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11801
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4118
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 146
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 206
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4733
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
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  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3188
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 211
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 17
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 321
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 154
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 321
  bin: 2.25e1
  variant carriers: 0
num of homozygotes: 0
population: East Asian
population: European (Finnish)
population: Latino
population: Other
population: African
population: European (Non-Finnish)
population: South Asian
reference allele: C
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: MQ
site quality: QD
site quality: MQRankSum
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: DP
site quality: FS
site quality: ReadPosRankSum

15-42457171-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457171
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457171
    reference: chr 15
allele count: 1
allele frequency: 8.263779852904718e-6
allele num: 121010
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.905G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.177G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.482+23G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1930+23G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1897+23G>A
  variant of: http://identifiers.org/hgnc/20593
canonical: false
consequence: non coding transcript exon
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 4493
  bin: 4.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1642
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 586
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10360
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 706
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7376
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11352
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2658
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10031
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7081
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 180
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 336
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 389
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 823
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 321
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 217
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 504
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1116
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 535
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4120
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2673
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 110
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 118
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 150
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4944
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3176
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 237
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 272
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5711
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 14
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 173
  bin: 2.75e1
  variant carriers: 0
num of homozygotes: 0
population: Other
population: European (Finnish)
population: East Asian
population: European (Non-Finnish)
population: Latino
population: South Asian
population: African
reference allele: C
site quality: BaseQRankSum
site quality: VQSLOD
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: FS
site quality: QD
site quality: DP
site quality: MQ

15-42457172-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457172
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457172
    reference: chr 15
allele count: 1
allele frequency: 8.261049153242462e-6
allele num: 121050
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.482+22C>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1897+22C>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1930+22C>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.176C>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.904C>T
  variant of: http://identifiers.org/hgnc/20593
canonical: false
consequence: non coding transcript exon
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 172
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 258
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4494
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10400
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1116
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2657
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1643
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 389
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10029
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7190
  bin: 2.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 11359
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 706
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 823
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7374
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 217
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 321
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 437
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 535
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 586
  bin: 9.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 69
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2681
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 248
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4123
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 187
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4761
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 143
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3198
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 70
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 176
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4952
  bin: 7.75e1
  variant carriers: 0
num of homozygotes: 0
population: European (Non-Finnish)
population: Other
population: Latino
population: South Asian
population: African
population: European (Finnish)
population: East Asian
reference allele: G
site quality: ReadPosRankSum
site quality: MQ
site quality: VQSLOD
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: FS
site quality: QD
site quality: ClippingRankSum
site quality: MQRankSum
site quality: DP

15-42457173-G-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457173
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457173
    reference: chr 15
allele count: 1
allele frequency: 8.260776182530111e-6
allele num: 121054
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.482+21C>G
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1930+21C>G
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.903C>G
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.175C>G
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1897+21C>G
  variant of: http://identifiers.org/hgnc/20593
canonical: false
consequence: non coding transcript exon
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 166
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 535
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7374
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 823
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 215
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 380
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11378
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10416
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 587
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 10034
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1642
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 321
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 217
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4494
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1116
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7257
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 705
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 389
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2657
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4953
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5754
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 151
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4122
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2681
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 59
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 158
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 130
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12560
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 60
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4761
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 93
  bin: 4.75e1
  variant carriers: 0
num of homozygotes: 0
population: South Asian
population: European (Non-Finnish)
population: Latino
population: Other
population: East Asian
population: African
population: European (Finnish)
reference allele: G
site quality: VQSLOD
site quality: QD
site quality: ClippingRankSum
site quality: FS
site quality: MQ
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: DP

15-42457181-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457181
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457181
    reference: chr 15
allele count: 1
allele frequency: 8.252050634582693e-6
allele num: 121182
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.167T>C
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.482+13T>C
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1930+13T>C
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.895T>C
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1897+13T>C
  variant of: http://identifiers.org/hgnc/20593
canonical: false
consequence: non coding transcript exon
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 111
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11414
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7410
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1116
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1641
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10040
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 86
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2657
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7377
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 321
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4494
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 163
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10619
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 389
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 705
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 823
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 588
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 217
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 535
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 40
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 61
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 54
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 129
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 36
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2684
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 71
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12956
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 62
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4124
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3220
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 26
  bin: 4.25e1
  variant carriers: 0
num of homozygotes: 0
population: Latino
population: East Asian
population: Other
population: European (Finnish)
population: African
population: European (Non-Finnish)
population: South Asian
reference allele: A
site quality: BaseQRankSum
site quality: MQRankSum
site quality: MQ
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: QD
site quality: FS
site quality: DP
site quality: ReadPosRankSum

15-42457183-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457183
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457183
    reference: chr 15
allele count: 1
allele frequency: 8.250144377526608e-6
allele num: 121210
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.482+11T>C
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.893T>C
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.165T>C
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1897+11T>C
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1930+11T>C
  variant of: http://identifiers.org/hgnc/20593
canonical: false
consequence: non coding transcript exon
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1642
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10036
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 535
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11422
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 706
  bin: 7.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 4494
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 587
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 69
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 823
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 389
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7442
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2657
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 99
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 137
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1116
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 217
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 321
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10638
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7376
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5807
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4763
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3220
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 49
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 53
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 59
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2682
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 38
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 116
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21704
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 31
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 7.5e0
  variant carriers: 0
num of homozygotes: 0
population: South Asian
population: East Asian
population: European (Non-Finnish)
population: Other
population: European (Finnish)
population: African
population: Latino
reference allele: A
site quality: MQRankSum
site quality: VQSLOD
site quality: DP
site quality: InbreedingCoeff
site quality: QD
site quality: ClippingRankSum
site quality: MQ
site quality: FS
site quality: BaseQRankSum
site quality: ReadPosRankSum

15-42457184-G-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457184
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457184
    reference: chr 15
allele count: 3
allele frequency: 2.475043313257982e-5
allele num: 121210
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.482+10C>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1930+10C>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1897+10C>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.164C>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.892C>A
  variant of: http://identifiers.org/hgnc/20593
canonical: false
consequence: non coding transcript exon
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 705
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 95
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 134
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4495
  bin: 4.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 587
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 823
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1643
  bin: 5.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 10037
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 65
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 389
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 535
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7441
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10645
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7379
  bin: 4.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 321
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 217
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11421
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1116
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2658
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 57
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5810
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13048
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 26
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 36
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4762
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4969
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 28
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 51
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 111
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 49
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21
  bin: 4.25e1
  variant carriers: 0
num of homozygotes: 0
population: South Asian
population: European (Finnish)
population: Other
population: European (Non-Finnish)
population: Latino
population: East Asian
population: African
reference allele: G
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: FS
site quality: MQ
site quality: DP
site quality: BaseQRankSum
site quality: QD
site quality: ClippingRankSum

15-42457190-G-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457190
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457190
    reference: chr 15
allele count: 3
allele frequency: 2.474063566939913e-5
allele num: 121258
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.886C>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.482+4C>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1897+4C>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1930+4C>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.158C>A
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: splice region
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 7378
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10729
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 535
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 218
  bin: 9.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7436
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 588
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11430
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4497
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 75
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10039
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 822
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 81
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1116
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 389
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 705
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2659
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 321
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1642
  bin: 5.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 5830
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 32
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13114
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4977
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4126
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 93
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2682
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 27
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 22
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 35
  bin: 2.75e1
  variant carriers: 0
hgvs: c.1897+4C>A
num of homozygotes: 0
population: East Asian
population: Latino
population: European (Finnish)
population: African
population: Other
population: South Asian
population: European (Non-Finnish)
reference allele: G
site quality: DP
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: QD
site quality: ClippingRankSum
site quality: VQSLOD
site quality: MQRankSum
site quality: MQ
site quality: ReadPosRankSum
site quality: FS

http://identifiers.org/exac.variant/15-42457197-C-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457197
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457197
    reference: chr 15
allele count: 1
allele frequency: 8.243887157672586e-6
allele num: 121302
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.479G>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1927G>T
  hgvsp: ENSP00000335193.5:p.Ala643Ser
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1894G>T
  hgvsp: ENSP00000326534.5:p.Ala632Ser
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.879G>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.151G>T
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 823
  bin: 6.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 4494
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 535
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11459
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2659
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7382
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10818
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7387
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 217
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 21
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1641
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10051
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 54
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 389
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 321
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1116
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 588
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 705
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2682
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4766
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 18
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 19
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13152
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4977
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 15
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 35
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4126
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
hgvs: p.Ala632Ser
num of homozygotes: 0
population: African
population: Other
population: Latino
population: East Asian
population: European (Non-Finnish)
population: South Asian
population: European (Finnish)
reference allele: C
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: DP
site quality: QD
site quality: FS
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: MQ
site quality: MQRankSum

15-42457209-G-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457209
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457209
    reference: chr 15
allele count: 1
allele frequency: 8.239539904091756e-6
allele num: 121366
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1915C>A
  hgvsp: ENSP00000335193.5:p.Leu639Met
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1882C>A
  hgvsp: ENSP00000326534.5:p.Leu628Met
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.867C>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.139C>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.467C>A
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 11458
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 389
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10045
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7391
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 22
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1116
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 535
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 705
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 217
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4496
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1642
  bin: 5.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 10890
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7380
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2659
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 321
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 588
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 822
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21706
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 4983
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 27
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4764
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4126
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3230
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2682
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 2.75e1
  variant carriers: 0
hgvs: p.Leu628Met
num of homozygotes: 0
population: European (Non-Finnish)
population: Other
population: European (Finnish)
population: African
population: South Asian
population: East Asian
population: Latino
reference allele: G
site quality: InbreedingCoeff
site quality: DP
site quality: BaseQRankSum
site quality: VQSLOD
site quality: MQRankSum
site quality: MQ
site quality: FS
site quality: QD
site quality: ClippingRankSum
site quality: ReadPosRankSum

15-42457216-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457216
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457216
    reference: chr 15
allele count: 3
allele frequency: 2.47161759132627e-5
allele num: 121378
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1908G>A
  hgvsp: ENST00000348544.4:c.1908G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.460G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1875G>A
  hgvsp: ENST00000318006.5:c.1875G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.132G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.860G>A
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 824
  bin: 6.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 535
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7380
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 390
  bin: 8.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 705
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10045
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7392
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11462
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10899
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1642
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 588
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 217
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1116
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 321
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2659
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4492
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4764
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4985
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4125
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5860
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 22
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 3.75e1
  variant carriers: 0
hgvs: p.Glu625Glu
num of homozygotes: 0
population: African
population: European (Finnish)
population: European (Non-Finnish)
population: Other
population: East Asian
population: South Asian
population: Latino
reference allele: C
site quality: ClippingRankSum
site quality: QD
site quality: DP
site quality: MQ
site quality: FS
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: BaseQRankSum
site quality: MQRankSum
site quality: InbreedingCoeff

15-42457229-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457229
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457229
    reference: chr 15
allele count: 55
allele frequency: 4.530925626915346e-4
allele num: 121388
alternate allele: T
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1862G>A
  hgvsp: ENSP00000326534.5:p.Gly621Asp
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.119G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.847G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.447G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1895G>A
  hgvsp: ENSP00000335193.5:p.Gly632Asp
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 605
  bin: 9.75e1
  variant carriers: 18
genotype depth: GenotypeDepth
  all individuals: 10039
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11465
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10906
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 710
  bin: 7.25e1
  variant carriers: 6
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 324
  bin: 8.75e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 221
  bin: 9.25e1
  variant carriers: 4
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4492
  bin: 4.75e1
  variant carriers: 5
genotype depth: GenotypeDepth
  all individuals: 1118
  bin: 6.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 12
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 824
  bin: 6.75e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 7370
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 390
  bin: 8.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 7376
  bin: 4.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1647
  bin: 5.75e1
  variant carriers: 6
genotype depth: GenotypeDepth
  all individuals: 2659
  bin: 5.25e1
  variant carriers: 5
genotype depth: GenotypeDepth
  all individuals: 533
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2683
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3224
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13309
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4764
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 3.25e1
  variant carriers: 0
hgvs: p.Gly621Asp
num of homozygotes: 0
population: East Asian
population: European (Non-Finnish)
population: European (Finnish)
population: African
population: Other
population: South Asian
population: Latino
reference allele: C
site quality: QD
site quality: BaseQRankSum
site quality: VQSLOD
site quality: MQRankSum
site quality: ClippingRankSum
site quality: FS
site quality: DP
site quality: MQ
site quality: InbreedingCoeff
site quality: ReadPosRankSum

15-42457231-T-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457231
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457231
    reference: chr 15
allele count: 19
allele frequency: 1.565177276921049e-4
allele num: 121392
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.445A>C
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1893A>C
  hgvsp: ENSP00000335193.5:p.Gln631His
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.845A>C
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.117A>C
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1860A>C
  hgvsp: ENSP00000326534.5:p.Gln620His
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 533
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10915
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 708
  bin: 7.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 323
  bin: 8.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11474
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4492
  bin: 4.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 7373
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1120
  bin: 6.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 600
  bin: 9.75e1
  variant carriers: 7
genotype depth: GenotypeDepth
  all individuals: 220
  bin: 9.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 823
  bin: 6.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2652
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1641
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10040
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 391
  bin: 8.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 7377
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4119
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5864
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4767
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3229
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2686
  bin: 8.75e1
  variant carriers: 0
hgvs: p.Gln620His
num of homozygotes: 0
population: European (Non-Finnish)
population: Other
population: Latino
population: South Asian
population: African
population: European (Finnish)
population: East Asian
reference allele: T
site quality: QD
site quality: MQ
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: FS
site quality: DP
site quality: VQSLOD
site quality: ReadPosRankSum
site quality: ClippingRankSum
site quality: MQRankSum

http://identifiers.org/exac.variant/15-42457234-C-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457234
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457234
    reference: chr 15
allele count: 1
allele frequency: 8.237503706876667e-6
allele num: 121396
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.842G>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1857G>T
  hgvsp: ENST00000318006.5:c.1857G>T(p.%3D)
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.442G>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.114G>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1890G>T
  hgvsp: ENST00000348544.4:c.1890G>T(p.%3D)
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 7381
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2654
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1642
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10915
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10047
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11478
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1118
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 822
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4492
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 706
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 218
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 389
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 533
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 594
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 321
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7372
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4771
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4121
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5865
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13318
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6
  bin: 5.75e1
  variant carriers: 0
hgvs: p.Val619Val
num of homozygotes: 0
population: East Asian
population: African
population: Latino
population: European (Non-Finnish)
population: European (Finnish)
population: South Asian
population: Other
reference allele: C
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: DP
site quality: VQSLOD
site quality: FS
site quality: MQRankSum
site quality: QD
site quality: MQ
site quality: ReadPosRankSum

15-42457236-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457236
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457236
    reference: chr 15
allele count: 87
allele frequency: 7.166628224982701e-4
allele num: 121396
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1888G>A
  hgvsp: ENSP00000335193.5:p.Val630Met
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.840G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.112G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1855G>A
  hgvsp: ENSP00000326534.5:p.Val619Met
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.440G>A
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 221
  bin: 9.25e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 7378
  bin: 4.25e1
  variant carriers: 4
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 713
  bin: 7.25e1
  variant carriers: 10
genotype depth: GenotypeDepth
  all individuals: 4492
  bin: 4.75e1
  variant carriers: 6
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1646
  bin: 5.75e1
  variant carriers: 5
genotype depth: GenotypeDepth
  all individuals: 11467
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 323
  bin: 8.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 7349
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 602
  bin: 9.75e1
  variant carriers: 10
genotype depth: GenotypeDepth
  all individuals: 1125
  bin: 6.25e1
  variant carriers: 7
genotype depth: GenotypeDepth
  all individuals: 10903
  bin: 2.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 540
  bin: 7.75e1
  variant carriers: 8
genotype depth: GenotypeDepth
  all individuals: 2659
  bin: 5.25e1
  variant carriers: 9
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10033
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 396
  bin: 8.25e1
  variant carriers: 7
genotype depth: GenotypeDepth
  all individuals: 836
  bin: 6.75e1
  variant carriers: 14
genotype quality: GenotypeQuality
  all individuals: 21750
  bin: 9.75e1
  variant carriers: 87
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4119
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13304
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5853
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4978
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
hgvs: p.Val619Met
num of homozygotes: 0
population: East Asian
population: European (Finnish)
population: European (Non-Finnish)
population: South Asian
population: Other
population: African
population: Latino
reference allele: C
site quality: BaseQRankSum
site quality: MQ
site quality: ClippingRankSum
site quality: DP
site quality: QD
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: VQSLOD
site quality: FS

15-42457238-T-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457238
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457238
    reference: chr 15
allele count: 1
allele frequency: 8.237367996177861e-6
allele num: 121398
alternate allele: C
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1853A>G
  hgvsp: ENSP00000326534.5:p.Lys618Arg
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.110A>G
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.838A>G
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1886A>G
  hgvsp: ENSP00000335193.5:p.Lys629Arg
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.438A>G
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 824
  bin: 6.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1118
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10920
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4495
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11484
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7387
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10043
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7356
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 703
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2655
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 390
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 533
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 219
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1645
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 322
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 592
  bin: 9.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4982
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3224
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4126
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13328
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5866
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 3.25e1
  variant carriers: 0
hgvs: p.Lys618Arg
num of homozygotes: 0
population: Other
population: East Asian
population: South Asian
population: European (Non-Finnish)
population: European (Finnish)
population: African
population: Latino
reference allele: T
site quality: BaseQRankSum
site quality: MQ
site quality: DP
site quality: FS
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: VQSLOD
site quality: ReadPosRankSum
site quality: ClippingRankSum
site quality: QD

15-42457260-G-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457260
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457260
    reference: chr 15
allele count: 1
allele frequency: 8.236689509752241e-6
allele num: 121408
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.816C>G
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1831C>G
  hgvsp: ENSP00000326534.5:p.Leu611Val
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.416C>G
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1864C>G
  hgvsp: ENSP00000335193.5:p.Leu622Val
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.88C>G
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 219
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10927
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1645
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10042
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 823
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 533
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 703
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1118
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7388
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11483
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 390
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2655
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7358
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 593
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 4494
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 322
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2688
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3221
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13346
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4980
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 5.25e1
  variant carriers: 0
hgvs: p.Leu611Val
num of homozygotes: 0
population: Other
population: European (Finnish)
population: African
population: European (Non-Finnish)
population: Latino
population: South Asian
population: East Asian
reference allele: G
site quality: DP
site quality: MQRankSum
site quality: QD
site quality: FS
site quality: ReadPosRankSum
site quality: BaseQRankSum
site quality: VQSLOD
site quality: ClippingRankSum
site quality: MQ
site quality: InbreedingCoeff

15-42457265-T-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457265
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457265
    reference: chr 15
allele count: 4
allele frequency: 3.294730079238259e-5
allele num: 121406
alternate allele: G
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1826A>C
  hgvsp: ENSP00000326534.5:p.Asn609Thr
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.411A>C
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1859A>C
  hgvsp: ENSP00000335193.5:p.Asn620Thr
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.83A>C
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.811A>C
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7355
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1118
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 704
  bin: 7.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2655
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4494
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10040
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 219
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 322
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 823
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 535
  bin: 7.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 10932
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11480
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 390
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 593
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 7387
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1645
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13347
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4769
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3222
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2688
  bin: 8.75e1
  variant carriers: 0
hgvs: p.Asn609Thr
num of homozygotes: 0
population: East Asian
population: Latino
population: South Asian
population: African
population: European (Finnish)
population: Other
population: European (Non-Finnish)
reference allele: T
site quality: MQ
site quality: FS
site quality: ClippingRankSum
site quality: ReadPosRankSum
site quality: DP
site quality: MQRankSum
site quality: QD
site quality: BaseQRankSum
site quality: VQSLOD
site quality: InbreedingCoeff

15-42457266-T-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457266
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457266
    reference: chr 15
allele count: 1
allele frequency: 8.236825198095647e-6
allele num: 121406
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1858A>C
  hgvsp: ENSP00000335193.5:p.Asn620His
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.410A>C
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1825A>C
  hgvsp: ENSP00000326534.5:p.Asn609His
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.82A>C
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.810A>C
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 7352
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1646
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 390
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2656
  bin: 5.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 11482
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 219
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 322
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10933
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10040
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 592
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7387
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 823
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4495
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 703
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 533
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1118
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3222
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5866
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4124
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21690
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 2688
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 2.75e1
  variant carriers: 0
hgvs: p.Asn609His
num of homozygotes: 0
population: South Asian
population: Latino
population: East Asian
population: Other
population: African
population: European (Non-Finnish)
population: European (Finnish)
reference allele: T
site quality: MQRankSum
site quality: MQ
site quality: ReadPosRankSum
site quality: QD
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: VQSLOD
site quality: FS
site quality: DP

15-42457274-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457274
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457274
    reference: chr 15
allele count: 2
allele frequency: 1.647365039619129e-5
allele num: 121406
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.802G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1850G>A
  hgvsp: ENSP00000335193.5:p.Arg617Gln
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.74G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1817G>A
  hgvsp: ENSP00000326534.5:p.Arg606Gln
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.402G>A
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 703
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 533
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 593
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1647
  bin: 5.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 10041
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7347
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10935
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 219
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 823
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7388
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4497
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1118
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 390
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11481
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 322
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2654
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5863
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13343
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3223
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2687
  bin: 8.75e1
  variant carriers: 0
hgvs: p.Arg606Gln
num of homozygotes: 0
population: Latino
population: European (Non-Finnish)
population: Other
population: East Asian
population: African
population: South Asian
population: European (Finnish)
reference allele: C
site quality: MQRankSum
site quality: BaseQRankSum
site quality: FS
site quality: ReadPosRankSum
site quality: QD
site quality: VQSLOD
site quality: MQ
site quality: InbreedingCoeff
site quality: DP
site quality: ClippingRankSum

15-42457275-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457275
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457275
    reference: chr 15
allele count: 21
allele frequency: 1.729733291600086e-4
allele num: 121406
alternate allele: A
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1816C>T
  hgvsp: ENSP00000326534.5:p.Arg606Trp
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.401C>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.801C>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.73C>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1849C>T
  hgvsp: ENSP00000335193.5:p.Arg617Trp
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 534
  bin: 7.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1120
  bin: 6.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 827
  bin: 6.75e1
  variant carriers: 4
genotype depth: GenotypeDepth
  all individuals: 7344
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11480
  bin: 3.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2655
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10930
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 392
  bin: 8.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 600
  bin: 9.75e1
  variant carriers: 8
genotype depth: GenotypeDepth
  all individuals: 7383
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4493
  bin: 4.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 10041
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 219
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1646
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 705
  bin: 7.25e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 323
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5859
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13342
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4980
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4767
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2686
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 5.75e1
  variant carriers: 0
hgvs: p.Arg606Trp
num of homozygotes: 0
population: Other
population: European (Finnish)
population: Latino
population: European (Non-Finnish)
population: East Asian
population: African
population: South Asian
reference allele: G
site quality: FS
site quality: DP
site quality: MQRankSum
site quality: QD
site quality: BaseQRankSum
site quality: VQSLOD
site quality: ReadPosRankSum
site quality: InbreedingCoeff
site quality: MQ
site quality: ClippingRankSum

15-42457276-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457276
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457276
    reference: chr 15
allele count: 1
allele frequency: 8.236825198095647e-6
allele num: 121406
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.800T>C
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.400T>C
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1815T>C
  hgvsp: ENST00000318006.5:c.1815T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1848T>C
  hgvsp: ENST00000348544.4:c.1848T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.72T>C
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 534
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10046
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4492
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 592
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1646
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11483
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 702
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2655
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7386
  bin: 4.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1119
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 219
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 323
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 390
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 824
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10936
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7345
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4981
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3222
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2687
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4770
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21687
  bin: 9.75e1
  variant carriers: 1
hgvs: p.Ser605Ser
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: A
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: DP
site quality: FS
site quality: MQ
site quality: MQRankSum
site quality: BaseQRankSum
site quality: VQSLOD
site quality: QD
site quality: ReadPosRankSum

15-42457290-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457290
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457290
    reference: chr 15
allele count: 1
allele frequency: 8.237232289950576e-6
allele num: 121400
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.386G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.58G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1834G>A
  hgvsp: ENSP00000335193.5:p.Glu612Lys
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1801G>A
  hgvsp: ENSP00000326534.5:p.Glu601Lys
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.786G>A
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 10044
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1646
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 593
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 2655
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11482
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 219
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7385
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 390
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 534
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 824
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4492
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1119
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 702
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10940
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7327
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 323
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4982
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4127
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2687
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3218
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21686
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 16
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13336
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
hgvs: p.Glu601Lys
num of homozygotes: 0
population: Latino
population: European (Non-Finnish)
population: African
population: South Asian
population: East Asian
population: Other
population: European (Finnish)
reference allele: C
site quality: VQSLOD
site quality: DP
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: QD
site quality: FS
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: ClippingRankSum
site quality: MQ

15-42457299-G-GGA
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457299
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457301
    reference: chr 15
allele count: 1
allele frequency: 8.238182327451271e-6
allele num: 121386
alternate allele: GGA
annotation: Annotation
  canonical: true
  consequence: frameshift_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1790_1791dupTC
  hgvsp: ENSP00000326534.5:p.His598SerfsTer15
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.375_376dupTC
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: frameshift_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1823_1824dupTC
  hgvsp: ENSP00000335193.5:p.His609SerfsTer15
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.775_776dupTC
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.47_48dupTC
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: frameshift
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1646
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 824
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 219
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10936
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7386
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11479
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1119
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7303
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 390
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2655
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4492
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 702
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 592
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 324
  bin: 8.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 10045
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 534
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 33
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3215
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4979
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 4.75e1
  variant carriers: 0
hgvs: p.His598SerfsTer15
num of homozygotes: 0
population: European (Finnish)
population: African
population: Latino
population: European (Non-Finnish)
population: Other
population: South Asian
population: East Asian
reference allele: G
site quality: FS
site quality: QD
site quality: MQRankSum
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: DP
site quality: ReadPosRankSum
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: MQ

15-42457304-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457304
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457304
    reference: chr 15
allele count: 1
allele frequency: 8.239268352970255e-6
allele num: 121370
alternate allele: G
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1787T>C
  hgvsp: ENSP00000326534.5:p.Ile596Thr
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1820T>C
  hgvsp: ENSP00000335193.5:p.Ile607Thr
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.372T>C
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.44T>C
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.772T>C
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2654
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1120
  bin: 6.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 702
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10921
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1646
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10043
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7294
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7387
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 592
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4492
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 534
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 323
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 824
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 390
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11480
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 219
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2686
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 51
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21685
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 4128
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4979
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4771
  bin: 8.25e1
  variant carriers: 0
hgvs: p.Ile596Thr
num of homozygotes: 0
population: African
population: European (Non-Finnish)
population: East Asian
population: South Asian
population: Other
population: Latino
population: European (Finnish)
reference allele: A
site quality: VQSLOD
site quality: ReadPosRankSum
site quality: FS
site quality: DP
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: MQ
site quality: QD
site quality: BaseQRankSum

15-42457317-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457317
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457317
    reference: chr 15
allele count: 1
allele frequency: 8.241577108195424e-6
allele num: 121336
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.365-6C>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.759C>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1780-6C>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1813-6C>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.37-6C>T
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: splice region
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 157
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 219
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 390
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7168
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 534
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10899
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10042
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2654
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11468
  bin: 3.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1646
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 53
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4493
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1119
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 35
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 592
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 702
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7387
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 323
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 824
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2685
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3201
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 18
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 14
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 36
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 35
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4128
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13121
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 30
  bin: 5.75e1
  variant carriers: 0
hgvs: c.1780-6C>T
num of homozygotes: 0
population: South Asian
population: East Asian
population: African
population: European (Finnish)
population: Latino
population: Other
population: European (Non-Finnish)
reference allele: G
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: VQSLOD
site quality: MQRankSum
site quality: DP
site quality: QD
site quality: MQ
site quality: ReadPosRankSum
site quality: FS
site quality: BaseQRankSum

15-42457325-T-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457325
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457325
    reference: chr 15
allele count: 1
allele frequency: 8.244294947896055e-6
allele num: 121296
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.365-14A>G
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.751A>G
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1813-14A>G
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1780-14A>G
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.37-14A>G
  variant of: http://identifiers.org/hgnc/20593
canonical: false
consequence: non coding transcript exon
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 138
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1646
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 824
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7384
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 289
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4492
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1119
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 390
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 54
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11448
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 323
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 219
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 592
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2654
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7010
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 703
  bin: 7.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 10039
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 534
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10846
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3194
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 76
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 17
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 30
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21682
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 197
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12911
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4764
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4972
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 25
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4127
  bin: 9.25e1
  variant carriers: 0
num of homozygotes: 0
population: Other
population: South Asian
population: Latino
population: East Asian
population: European (Finnish)
population: European (Non-Finnish)
population: African
reference allele: T
site quality: FS
site quality: ClippingRankSum
site quality: VQSLOD
site quality: QD
site quality: InbreedingCoeff
site quality: MQ
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: BaseQRankSum
site quality: DP

15-42457348-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457348
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457348
    reference: chr 15
allele count: 1
allele frequency: 8.255320554097116e-6
allele num: 121134
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.37-37G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.728G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1780-37G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1813-37G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.365-37G>A
  variant of: http://identifiers.org/hgnc/20593
canonical: false
consequence: non coding transcript exon
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 7387
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 747
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 219
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1120
  bin: 6.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 4491
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 592
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 95
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 825
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 390
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11318
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10101
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5900
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1631
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1646
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 702
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  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10027
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2653
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 534
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 323
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 19
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  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11
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genotype quality: GenotypeQuality
  all individuals: 2678
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genotype quality: GenotypeQuality
  all individuals: 423
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genotype quality: GenotypeQuality
  all individuals: 26
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genotype quality: GenotypeQuality
  all individuals: 10813
  bin: 6.25e1
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genotype quality: GenotypeQuality
  all individuals: 230
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genotype quality: GenotypeQuality
  all individuals: 322
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4117
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genotype quality: GenotypeQuality
  all individuals: 5512
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genotype quality: GenotypeQuality
  all individuals: 21676
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genotype quality: GenotypeQuality
  all individuals: 637
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genotype quality: GenotypeQuality
  all individuals: 611
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  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4912
  bin: 7.75e1
  variant carriers: 0
num of homozygotes: 0
population: European (Non-Finnish)
population: European (Finnish)
population: Latino
population: African
population: East Asian
population: Other
population: South Asian
reference allele: C
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: BaseQRankSum
site quality: FS
site quality: ClippingRankSum
site quality: DP
site quality: MQRankSum
site quality: VQSLOD
site quality: MQ
site quality: QD

15-42457359-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457359
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457359
    reference: chr 15
allele count: 1
allele frequency: 8.261322141995606e-6
allele num: 121046
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1813-48G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1780-48G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.717G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.37-48G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.365-48G>A
  variant of: http://identifiers.org/hgnc/20593
canonical: false
consequence: non coding transcript exon
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 4492
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 824
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2654
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9979
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 219
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6556
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  variant carriers: 0
genotype depth: GenotypeDepth
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  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 592
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 323
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1646
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 119
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  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10955
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  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 702
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  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9314
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 792
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  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1119
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
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  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 534
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  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 390
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  variant carriers: 0
genotype depth: GenotypeDepth
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  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 26
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  variant carriers: 0
genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
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  variant carriers: 0
genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
  all individuals: 2676
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genotype quality: GenotypeQuality
  all individuals: 773
  bin: 3.25e1
  variant carriers: 0
num of homozygotes: 0
population: Latino
population: European (Finnish)
population: European (Non-Finnish)
population: African
population: Other
population: South Asian
population: East Asian
reference allele: C
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: DP
site quality: BaseQRankSum
site quality: FS
site quality: MQ
site quality: ClippingRankSum
site quality: MQRankSum
site quality: QD

15-42457870-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457870
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457870
    reference: chr 15
allele count: 2
allele frequency: 1.657907389293234e-5
allele num: 120634
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.36+46C>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1812+46C>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1779+46C>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.206C>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.364+46C>T
  variant of: http://identifiers.org/hgnc/20593
canonical: false
consequence: non coding transcript exon
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 334
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6889
  bin: 3.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 415
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 190
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  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1194
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
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  variant carriers: 0
genotype depth: GenotypeDepth
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  variant carriers: 0
genotype depth: GenotypeDepth
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  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
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  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
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  variant carriers: 0
genotype depth: GenotypeDepth
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  variant carriers: 0
genotype depth: GenotypeDepth
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  variant carriers: 0
genotype depth: GenotypeDepth
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  variant carriers: 0
genotype depth: GenotypeDepth
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  variant carriers: 0
genotype depth: GenotypeDepth
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  variant carriers: 0
genotype depth: GenotypeDepth
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  variant carriers: 0
genotype depth: GenotypeDepth
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  variant carriers: 0
genotype depth: GenotypeDepth
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  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 598
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
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  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3657
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  variant carriers: 0
genotype quality: GenotypeQuality
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  variant carriers: 0
genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
  all individuals: 4094
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10605
  bin: 9.75e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 25
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 640
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8324
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1855
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 580
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 461
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 259
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 348
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21049
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 51
  bin: 1.75e1
  variant carriers: 0
num of homozygotes: 0
population: European (Non-Finnish)
population: Other
population: European (Finnish)
population: South Asian
population: East Asian
population: Latino
population: African
reference allele: G
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: FS
site quality: QD
site quality: ReadPosRankSum
site quality: BaseQRankSum
site quality: VQSLOD
site quality: MQ
site quality: DP

15-42457879-T-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457879
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457879
    reference: chr 15
allele count: 3
allele frequency: 2.485212982752622e-5
allele num: 120714
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.36+37A>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.364+37A>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1779+37A>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.197A>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1812+37A>T
  variant of: http://identifiers.org/hgnc/20593
canonical: false
consequence: non coding transcript exon
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 309
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 855
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 99
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 415
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 190
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2075
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 19535
  bin: 2.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 27
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 273
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 166
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9168
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6891
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3818
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 798
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13046
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 621
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 369
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 257
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 599
  bin: 6.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1195
  bin: 5.25e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 371
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 183
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 197
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10599
  bin: 9.75e1
  variant carriers: 3
genotype quality: GenotypeQuality
  all individuals: 402
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 384
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 203
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 19
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5086
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 201
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4089
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 23
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 239
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 18
  bin: 7.5e0
  variant carriers: 0
num of homozygotes: 0
population: Other
population: South Asian
population: African
population: European (Non-Finnish)
population: Latino
population: East Asian
population: European (Finnish)
reference allele: T
site quality: VQSLOD
site quality: DP
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: MQRankSum
site quality: FS
site quality: ClippingRankSum
site quality: ReadPosRankSum
site quality: QD
site quality: MQ

15-42457886-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457886
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457886
    reference: chr 15
allele count: 1
allele frequency: 8.283357078956959e-6
allele num: 120724
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.36+30G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1812+30G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.364+30G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.190G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1779+30G>A
  variant of: http://identifiers.org/hgnc/20593
canonical: false
consequence: non coding transcript exon
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 2076
  bin: 4.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 369
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 415
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9570
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 273
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 294
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 593
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1195
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 261
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 799
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 257
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 19
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6902
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3821
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13083
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 19726
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 99
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 166
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 190
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 598
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 23
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4081
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 113
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 22803
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8376
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 91
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3689
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 251
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1848
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 113
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5082
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 269
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 340
  bin: 2.25e1
  variant carriers: 0
num of homozygotes: 0
population: European (Finnish)
population: African
population: South Asian
population: European (Non-Finnish)
population: East Asian
population: Other
population: Latino
reference allele: C
site quality: ReadPosRankSum
site quality: FS
site quality: ClippingRankSum
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: MQ
site quality: QD
site quality: MQRankSum
site quality: DP

15-42457894-T-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457894
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457894
    reference: chr 15
allele count: 1
allele frequency: 8.273625337150233e-6
allele num: 120866
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1812+22A>G
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.182A>G
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1779+22A>G
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.36+22A>G
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.364+22A>G
  variant of: http://identifiers.org/hgnc/20593
canonical: false
consequence: non coding transcript exon
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 249
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1194
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 125
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 19842
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 598
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3816
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 273
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 799
  bin: 5.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 6890
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13086
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9871
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 190
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 257
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 166
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 378
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2075
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 415
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 369
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 99
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  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 23316
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 29
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  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 168
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 278
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  variant carriers: 0
genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
  all individuals: 40
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  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 55
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genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
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  variant carriers: 0
genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
  all individuals: 5100
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genotype quality: GenotypeQuality
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genotype quality: GenotypeQuality
  all individuals: 119
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genotype quality: GenotypeQuality
  all individuals: 4093
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  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8461
  bin: 6.75e1
  variant carriers: 0
num of homozygotes: 0
population: Latino
population: European (Non-Finnish)
population: African
population: East Asian
population: South Asian
population: European (Finnish)
population: Other
reference allele: T
site quality: FS
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: DP
site quality: MQRankSum
site quality: VQSLOD
site quality: QD
site quality: ReadPosRankSum
site quality: MQ
site quality: BaseQRankSum

http://identifiers.org/exac.variant/15-42457900-C-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457900
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457900
    reference: chr 15
allele count: 1
allele frequency: 8.267605866693123e-6
allele num: 120954
alternate allele: A
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1779+16G>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1812+16G>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.364+16G>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.176G>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.36+16G>T
  variant of: http://identifiers.org/hgnc/20593
canonical: false
consequence: non coding transcript exon
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 3819
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9910
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 416
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6898
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
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  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
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  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
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  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 190
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 799
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1195
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 212
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 369
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 166
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2074
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 275
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 257
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 252
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 598
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 14
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 112
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
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  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5099
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 234
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8487
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3708
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 88
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 37
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  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
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  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2710
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 90
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 28
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10600
  bin: 9.75e1
  variant carriers: 1
num of homozygotes: 0
population: Latino
population: South Asian
population: European (Non-Finnish)
population: Other
population: African
population: European (Finnish)
population: East Asian
reference allele: C
site quality: MQRankSum
site quality: FS
site quality: MQ
site quality: DP
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: VQSLOD
site quality: QD
site quality: InbreedingCoeff
site quality: ReadPosRankSum

15-42457900-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457900
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457900
    reference: chr 15
allele count: 4
allele frequency: 3.307042346677249e-5
allele num: 120954
alternate allele: T
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1779+16G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.364+16G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.176G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.36+16G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1812+16G>A
  variant of: http://identifiers.org/hgnc/20593
canonical: false
consequence: non coding transcript exon
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 13115
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3819
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 416
  bin: 6.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1195
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6898
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2074
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 166
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 212
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 19971
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 598
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9910
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 257
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 252
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 190
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 369
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 799
  bin: 5.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 81
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 275
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4091
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2710
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 112
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 90
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 29
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 234
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3708
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5099
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 88
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 23491
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 14
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10600
  bin: 9.75e1
  variant carriers: 4
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 1.75e1
  variant carriers: 0
num of homozygotes: 0
population: Latino
population: African
population: European (Non-Finnish)
population: European (Finnish)
population: East Asian
population: Other
population: South Asian
reference allele: C
site quality: MQRankSum
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: InbreedingCoeff
site quality: FS
site quality: QD
site quality: MQ
site quality: VQSLOD
site quality: DP
site quality: ClippingRankSum

15-42457927-T-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457927
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457927
    reference: chr 15
allele count: 3
allele frequency: 2.47537006782514e-5
allele num: 121194
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1801A>G
  hgvsp: ENSP00000335193.5:p.Ile601Val
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.353A>G
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.149A>G
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1768A>G
  hgvsp: ENSP00000326534.5:p.Ile590Val
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.25A>G
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1193
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 23
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6891
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 86
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13153
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 369
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3817
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 597
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 415
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20173
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 191
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 277
  bin: 9.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 10020
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 107
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 257
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 167
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2071
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 799
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 99
  bin: 9.25e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 1852
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4083
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 23851
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2713
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 119
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5103
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 38
  bin: 2.75e1
  variant carriers: 0
hgvs: p.Ile590Val
num of homozygotes: 0
population: Latino
population: East Asian
population: African
population: European (Finnish)
population: Other
population: European (Non-Finnish)
population: South Asian
reference allele: T
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: FS
site quality: DP
site quality: BaseQRankSum
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: MQ
site quality: QD

15-42457927-T-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457927
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457927
    reference: chr 15
allele count: 4
allele frequency: 3.300493423766853e-5
allele num: 121194
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.353A>C
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.25A>C
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1801A>C
  hgvsp: ENSP00000335193.5:p.Ile601Leu
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1768A>C
  hgvsp: ENSP00000326534.5:p.Ile590Leu
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.149A>C
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 191
  bin: 8.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 6891
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 107
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10020
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1193
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13153
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 597
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20173
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3817
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 799
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2071
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 23
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 99
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 86
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 167
  bin: 8.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 257
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 415
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 369
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 277
  bin: 9.75e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4083
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 119
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3713
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 23851
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8546
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5103
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
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  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 34
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1852
  bin: 8.75e1
  variant carriers: 0
hgvs: p.Ile590Leu
num of homozygotes: 0
population: African
population: Latino
population: European (Finnish)
population: South Asian
population: Other
population: East Asian
population: European (Non-Finnish)
reference allele: T
site quality: MQRankSum
site quality: BaseQRankSum
site quality: DP
site quality: ClippingRankSum
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: FS
site quality: QD
site quality: InbreedingCoeff
site quality: MQ

http://identifiers.org/exac.variant/15-42457930-C-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457930
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457930
    reference: chr 15
allele count: 2
allele frequency: 1.650083329208125e-5
allele num: 121206
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.146G>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1798G>T
  hgvsp: ENSP00000335193.5:p.Ala600Ser
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.22G>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.350G>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1765G>T
  hgvsp: ENSP00000326534.5:p.Ala589Ser
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 13159
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1194
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3817
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 257
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10023
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6891
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 369
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20178
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2071
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 77
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 799
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 30
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 273
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 99
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 415
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 192
  bin: 8.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 166
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 597
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8545
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 111
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 36
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2712
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5101
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4084
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 15
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 17
  bin: 3.75e1
  variant carriers: 0
hgvs: p.Ala589Ser
num of homozygotes: 0
population: East Asian
population: South Asian
population: Latino
population: European (Finnish)
population: Other
population: African
population: European (Non-Finnish)
reference allele: C
site quality: QD
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: DP
site quality: MQRankSum
site quality: VQSLOD
site quality: ReadPosRankSum
site quality: MQ
site quality: FS
site quality: BaseQRankSum

15-42457933-G-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457933
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457933
    reference: chr 15
allele count: 1
allele frequency: 8.249599894405122e-6
allele num: 121218
alternate allele: C
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1762C>G
  hgvsp: ENSP00000326534.5:p.Leu588Val
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.143C>G
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.19C>G
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1795C>G
  hgvsp: ENSP00000335193.5:p.Leu599Val
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.347C>G
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 3817
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13158
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1194
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 369
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6891
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 30
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 71
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2071
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 257
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 166
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20185
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 93
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10030
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 799
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 415
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 597
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 273
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 190
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 106
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 26
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 17
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4086
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8547
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5100
  bin: 7.75e1
  variant carriers: 0
hgvs: p.Leu588Val
num of homozygotes: 0
population: Other
population: East Asian
population: African
population: European (Non-Finnish)
population: South Asian
population: European (Finnish)
population: Latino
reference allele: G
site quality: ReadPosRankSum
site quality: FS
site quality: MQRankSum
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: QD
site quality: VQSLOD
site quality: MQ
site quality: DP
site quality: ClippingRankSum

http://identifiers.org/exac.variant/15-42457934-A-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457934
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457934
    reference: chr 15
allele count: 1
allele frequency: 8.249327679794096e-6
allele num: 121222
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1794T>G
  hgvsp: ENST00000348544.4:c.1794T>G(p.%3D)
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.346T>G
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1761T>G
  hgvsp: ENST00000318006.5:c.1761T>G(p.%3D)
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.18T>G
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.142T>G
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 274
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 166
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6890
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1194
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 799
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 415
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20184
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3817
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10034
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 69
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2071
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 92
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 189
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 369
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13159
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 597
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 257
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 30
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10592
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 5100
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3713
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 103
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 23885
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2712
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 34
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 24
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 1.75e1
  variant carriers: 0
hgvs: p.Gly587Gly
num of homozygotes: 0
population: East Asian
population: European (Finnish)
population: European (Non-Finnish)
population: Latino
population: African
population: South Asian
population: Other
reference allele: A
site quality: FS
site quality: VQSLOD
site quality: MQRankSum
site quality: ClippingRankSum
site quality: ReadPosRankSum
site quality: InbreedingCoeff
site quality: MQ
site quality: QD
site quality: DP
site quality: BaseQRankSum

15-42457937-C-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457937
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457937
    reference: chr 15
allele count: 1
allele frequency: 8.249599894405122e-6
allele num: 121218
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.343G>C
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1758G>C
  hgvsp: ENSP00000326534.5:p.Lys586Asn
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000561797
  gene symbol: VPS39
  hgvsc: ENST00000561797.1:n.15G>C
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1791G>C
  hgvsp: ENSP00000335193.5:p.Lys597Asn
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.139G>C
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 10026
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20185
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 93
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 66
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 189
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 35
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1195
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 415
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13160
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2071
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3818
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6890
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 257
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 166
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 597
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 800
  bin: 5.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 369
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 273
  bin: 9.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 25
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 32
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 23878
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2712
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5099
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 104
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 4.25e1
  variant carriers: 0
hgvs: p.Lys586Asn
num of homozygotes: 0
population: East Asian
population: Latino
population: African
population: European (Non-Finnish)
population: South Asian
population: European (Finnish)
population: Other
reference allele: C
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: FS
site quality: VQSLOD
site quality: QD
site quality: ClippingRankSum
site quality: MQ
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: DP

15-42457960-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457960
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457960
    reference: chr 15
allele count: 8
allele frequency: 6.597829314155642e-5
allele num: 121252
alternate allele: T
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1735G>A
  hgvsp: ENSP00000326534.5:p.Gly579Ser
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.320G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1768G>A
  hgvsp: ENSP00000335193.5:p.Gly590Ser
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.116G>A
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 76
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 100
  bin: 9.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 56
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 189
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6891
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2069
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3814
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 799
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10062
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1194
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 414
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 34
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13157
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20181
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 597
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 369
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 278
  bin: 9.75e1
  variant carriers: 5
genotype depth: GenotypeDepth
  all individuals: 167
  bin: 8.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 257
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 22
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1851
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 91
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5102
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 17
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 23894
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4081
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10595
  bin: 9.75e1
  variant carriers: 8
genotype quality: GenotypeQuality
  all individuals: 28
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2712
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3713
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12
  bin: 4.75e1
  variant carriers: 0
hgvs: p.Gly579Ser
num of homozygotes: 0
population: South Asian
population: European (Finnish)
population: Latino
population: African
population: East Asian
population: European (Non-Finnish)
population: Other
reference allele: C
site quality: DP
site quality: BaseQRankSum
site quality: QD
site quality: VQSLOD
site quality: ClippingRankSum
site quality: MQ
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: FS
site quality: InbreedingCoeff

15-42457961-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457961
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457961
    reference: chr 15
allele count: 5
allele frequency: 4.123167252156417e-5
allele num: 121266
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1767C>T
  hgvsp: ENST00000348544.4:c.1767C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.115C>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.319C>T
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1734C>T
  hgvsp: ENST00000318006.5:c.1734C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 71
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 257
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 798
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 597
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10075
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13160
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 53
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3814
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 278
  bin: 9.75e1
  variant carriers: 5
genotype depth: GenotypeDepth
  all individuals: 414
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 166
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 189
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6892
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2070
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20181
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1194
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 368
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 14
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 23930
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3715
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 28
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1851
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10588
  bin: 9.75e1
  variant carriers: 5
genotype quality: GenotypeQuality
  all individuals: 5103
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4081
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.25e1
  variant carriers: 0
hgvs: p.Leu578Leu
num of homozygotes: 0
population: South Asian
population: Other
population: Latino
population: African
population: European (Finnish)
population: East Asian
population: European (Non-Finnish)
reference allele: G
site quality: BaseQRankSum
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: QD
site quality: FS
site quality: VQSLOD
site quality: MQ
site quality: ReadPosRankSum
site quality: ClippingRankSum
site quality: DP

15-42457968-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 42457968
    reference: chr 15
  end: Position
    type: ExactPosition
    position: 42457968
    reference: chr 15
allele count: 1
allele frequency: 8.246878556466378e-6
allele num: 121258
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000335193
  ensembl transcript: ENST00000348544
  gene symbol: VPS39
  hgvsc: ENST00000348544.4:c.1760G>A
  hgvsp: ENSP00000335193.5:p.Arg587Gln
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000562258
  gene symbol: VPS39
  hgvsc: ENST00000562258.1:n.108G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000166887
  ensembl transcript: ENST00000563692
  gene symbol: VPS39
  hgvsc: ENST00000563692.1:n.312G>A
  variant of: http://identifiers.org/hgnc/20593
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000166887
  ensembl protein: ENSP00000326534
  ensembl transcript: ENST00000318006
  gene symbol: VPS39
  hgvsc: ENST00000318006.5:c.1727G>A
  hgvsp: ENSP00000326534.5:p.Arg576Gln
  variant of: http://identifiers.org/hgnc/20593
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 10078
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3813
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 189
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 368
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 59
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6890
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 72
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 98
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13154
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2071
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 257
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1194
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 414
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 597
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20180
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 798
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 274
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 166
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 14
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 92
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 16
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 23920
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1851
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 17
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2711
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8537
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3713
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4082
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 29
  bin: 2.75e1
  variant carriers: 0
hgvs: p.Arg576Gln
num of homozygotes: 0
population: Other
population: Latino
population: South Asian
population: African
population: East Asian
population: European (Non-Finnish)
population: European (Finnish)
reference allele: C
site quality: VQSLOD
site quality: FS
site quality: DP
site quality: ClippingRankSum
site quality: MQRankSum
site quality: BaseQRankSum
site quality: QD
site quality: InbreedingCoeff

GenotypeQuality
all individuals: 656
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 821
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 21
bin: 5.75e1
variant carriers: 0

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

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11562
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8648
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16506
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 9.611687812379854e-5
allele num: 10404
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 3
allele frequency: 4.496807266840543e-5
allele num: 66714
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 904
num of homozygotes: 0

DP
type: SiteQuality
SIO_000300: 1.739313e6

ClippingRankSum
type: SiteQuality
SIO_000300: -2.35e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 3.0e-4

MQ
type: SiteQuality
SIO_000300: 5.958e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 2.39e-1

VQSLOD
type: SiteQuality
SIO_000300: 1.8e0

FS
type: SiteQuality
SIO_000300: 2.559e0

MQRankSum
type: SiteQuality
SIO_000300: -1.0e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 2.09e0

QD
type: SiteQuality
SIO_000300: 1.334e1

GenotypeQuality
all individuals: 821
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 14
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 656
bin: 8.75e1
variant carriers: 0

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

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8648
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10404
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 904
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11562
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16506
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.498935755613514e-5
allele num: 66714
num of homozygotes: 0

ClippingRankSum
type: SiteQuality
SIO_000300: -2.35e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 2.09e0

MQRankSum
type: SiteQuality
SIO_000300: -1.0e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 3.0e-4

QD
type: SiteQuality
SIO_000300: 1.334e1

FS
type: SiteQuality
SIO_000300: 2.559e0

MQ
type: SiteQuality
SIO_000300: 5.958e1

VQSLOD
type: SiteQuality
SIO_000300: 1.8e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 2.39e-1

DP
type: SiteQuality
SIO_000300: 1.739313e6

GenotypeQuality
all individuals: 10
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 8748
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 40973
bin: 6.25e1
variant carriers: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10404
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16504
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 904
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 2
allele frequency: 2.997961386257345e-5
allele num: 66712
num of homozygotes: 0

East Asian
type: Population
allele count: 1
allele frequency: 1.156336725254394e-4
allele num: 8648
num of homozygotes: 0

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

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11562
num of homozygotes: 0

MQ
type: SiteQuality
SIO_000300: 5.931e1

ClippingRankSum
type: SiteQuality
SIO_000300: -6.14e-1

MQRankSum
type: SiteQuality
SIO_000300: -2.21e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -3.0e-4

QD
type: SiteQuality
SIO_000300: 1.254e1

FS
type: SiteQuality
SIO_000300: 9.91e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.09e0

VQSLOD
type: SiteQuality
SIO_000300: 1.71e0

BaseQRankSum
type: SiteQuality
SIO_000300: -7.38e-1

DP
type: SiteQuality
SIO_000300: 1.739001e6

GenotypeQuality
all individuals: 11
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 2599
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2149
bin: 9.75e1
variant carriers: 1

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11562
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16504
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 9.611687812379854e-5
allele num: 10404
num of homozygotes: 0

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

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8648
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 906
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66722
num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: -7.077e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 5.17e-1

MQRankSum
type: SiteQuality
SIO_000300: -1.64e-1

MQ
type: SiteQuality
SIO_000300: 5.815e1

FS
type: SiteQuality
SIO_000300: 3.547e0

DP
type: SiteQuality
SIO_000300: 1.738513e6

BaseQRankSum
type: SiteQuality
SIO_000300: -1.331e0

ClippingRankSum
type: SiteQuality
SIO_000300: -7.35e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.0e-4

QD
type: SiteQuality
SIO_000300: 1.453e1

GenotypeQuality
all individuals: 1642
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 816
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2148
bin: 9.75e1
variant carriers: 5

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10404
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 5
allele frequency: 7.494004796163069e-5
allele num: 66720
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16502
num of homozygotes: 0

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

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 906
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11562
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8650
num of homozygotes: 0

MQRankSum
type: SiteQuality
SIO_000300: -3.0e-2

VQSLOD
type: SiteQuality
SIO_000300: 1.7e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.0e-4

QD
type: SiteQuality
SIO_000300: 1.475e1

BaseQRankSum
type: SiteQuality
SIO_000300: 3.43e0

ClippingRankSum
type: SiteQuality
SIO_000300: 6.49e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: -2.79e-1

FS
type: SiteQuality
SIO_000300: 2.455e0

DP
type: SiteQuality
SIO_000300: 1.738445e6

MQ
type: SiteQuality
SIO_000300: 5.962e1

GenotypeQuality
all individuals: 10
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 12
bin: 3.75e1
variant carriers: 0

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

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

South Asian
type: Population
allele count: 10
allele frequency: 6.059871530723549e-4
allele num: 16502
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 906
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11562
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10404
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8650
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66716
num of homozygotes: 0

BaseQRankSum
type: SiteQuality
SIO_000300: -2.24e0

VQSLOD
type: SiteQuality
SIO_000300: 1.47e0

MQRankSum
type: SiteQuality
SIO_000300: 3.29e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

QD
type: SiteQuality
SIO_000300: 1.128e1

FS
type: SiteQuality
SIO_000300: 2.499e0

ClippingRankSum
type: SiteQuality
SIO_000300: 2.35e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 4.02e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -3.0e-4

DP
type: SiteQuality
SIO_000300: 1.738416e6

GenotypeQuality
all individuals: 41030
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2594
bin: 7.25e1
variant carriers: 0

GenotypeQuality
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bin: 8.75e1
variant carriers: 0

Latino
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allele frequency: 0.0e0
allele num: 11562
num of homozygotes: 0

African
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allele count: 0
allele frequency: 0.0e0
allele num: 10404
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European (Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

European (Non-Finnish)
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allele count: 6
allele frequency: 8.993075331994364e-5
allele num: 66718
num of homozygotes: 0

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

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

Other
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allele frequency: 0.0e0
allele num: 906
num of homozygotes: 0

ReadPosRankSum
type: SiteQuality
SIO_000300: 8.129999999999999e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -6.4e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.0e-4

MQRankSum
type: SiteQuality
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DP
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FS
type: SiteQuality
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VQSLOD
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MQ
type: SiteQuality
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QD
type: SiteQuality
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BaseQRankSum
type: SiteQuality
SIO_000300: -1.994e0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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bin: 6.25e1
variant carriers: 0

European (Non-Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 66708
num of homozygotes: 0

Other
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allele frequency: 0.0e0
allele num: 906
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African
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allele count: 0
allele frequency: 0.0e0
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num of homozygotes: 0

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

East Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 8648
num of homozygotes: 0

Latino
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allele count: 0
allele frequency: 0.0e0
allele num: 11562
num of homozygotes: 0

South Asian
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allele frequency: 6.06060606060606e-5
allele num: 16500
num of homozygotes: 0

QD
type: SiteQuality
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BaseQRankSum
type: SiteQuality
SIO_000300: -3.988e0

VQSLOD
type: SiteQuality
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MQ
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ReadPosRankSum
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MQRankSum
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FS
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ClippingRankSum
type: SiteQuality
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InbreedingCoeff
type: SiteQuality
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DP
type: SiteQuality
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GenotypeQuality
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bin: 3.25e1
variant carriers: 0

GenotypeQuality
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GenotypeQuality
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variant carriers: 0

Latino
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allele frequency: 0.0e0
allele num: 11562
num of homozygotes: 0

East Asian
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allele frequency: 0.0e0
allele num: 8648
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Other
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allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

African
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allele count: 0
allele frequency: 0.0e0
allele num: 10402
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European (Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 6610
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European (Non-Finnish)
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allele count: 1
allele frequency: 1.499115521842113e-5
allele num: 66706
num of homozygotes: 0

South Asian
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allele frequency: 0.0e0
allele num: 16498
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 5.753e0

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

ClippingRankSum
type: SiteQuality
SIO_000300: 5.639999999999999e-1

DP
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BaseQRankSum
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

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

East Asian
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allele frequency: 1.156871818602499e-4
allele num: 8644
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Latino
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allele frequency: 0.0e0
allele num: 11554
num of homozygotes: 0

European (Non-Finnish)
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allele count: 2
allele frequency: 2.99895036737142e-5
allele num: 66690
num of homozygotes: 0

South Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 16490
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African
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allele count: 0
allele frequency: 0.0e0
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Other
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allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 2.477e0

MQRankSum
type: SiteQuality
SIO_000300: 6.2e-2

ClippingRankSum
type: SiteQuality
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VQSLOD
type: SiteQuality
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InbreedingCoeff
type: SiteQuality
SIO_000300: -3.0e-4

DP
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BaseQRankSum
type: SiteQuality
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MQ
type: SiteQuality
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QD
type: SiteQuality
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ReadPosRankSum
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SIO_000300: 1.56e0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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variant carriers: 0

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

African
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allele count: 6
allele frequency: 5.774783445620789e-4
allele num: 10390
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South Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 16476
num of homozygotes: 0

European (Non-Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 66656
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

East Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 8646
num of homozygotes: 0

Latino
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allele count: 0
allele frequency: 0.0e0
allele num: 11554
num of homozygotes: 0

QD
type: SiteQuality
SIO_000300: 1.383e1

VQSLOD
type: SiteQuality
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ClippingRankSum
type: SiteQuality
SIO_000300: -4.66e-1

MQ
type: SiteQuality
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InbreedingCoeff
type: SiteQuality
SIO_000300: -2.0e-4

FS
type: SiteQuality
SIO_000300: 3.246e0

BaseQRankSum
type: SiteQuality
SIO_000300: -2.5e0

DP
type: SiteQuality
SIO_000300: 1.728328e6

ReadPosRankSum
type: SiteQuality
SIO_000300: 2.58e-1

MQRankSum
type: SiteQuality
SIO_000300: -1.37e-1

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 1

South Asian
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allele frequency: 6.070908207867897e-5
allele num: 16472
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66652
num of homozygotes: 0

African
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allele count: 0
allele frequency: 0.0e0
allele num: 10388
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East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8642
num of homozygotes: 0

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

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11556
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: 2.73e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

MQRankSum
type: SiteQuality
SIO_000300: 8.74e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 6.77e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.0e-4

QD
type: SiteQuality
SIO_000300: 9.9e0

FS
type: SiteQuality
SIO_000300: 0.0e0

DP
type: SiteQuality
SIO_000300: 1.727417e6

BaseQRankSum
type: SiteQuality
SIO_000300: -2.523e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 6.42e-1

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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variant carriers: 0

African
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allele count: 0
allele frequency: 0.0e0
allele num: 10380
num of homozygotes: 0

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

South Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 16460
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8638
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 2
allele frequency: 3.002011347602894e-5
allele num: 66622
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

Latino
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allele count: 0
allele frequency: 0.0e0
allele num: 11550
num of homozygotes: 0

BaseQRankSum
type: SiteQuality
SIO_000300: -2.037e0

MQ
type: SiteQuality
SIO_000300: 5.95e1

MQRankSum
type: SiteQuality
SIO_000300: 4.46e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: -7.07e-1

VQSLOD
type: SiteQuality
SIO_000300: 3.64e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 4.77e-1

DP
type: SiteQuality
SIO_000300: 1.724805e6

FS
type: SiteQuality
SIO_000300: 6.171e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.0e-4

QD
type: SiteQuality
SIO_000300: 1.161e1

GenotypeQuality
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variant carriers: 6

GenotypeQuality
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GenotypeQuality
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variant carriers: 0

Latino
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allele count: 0
allele frequency: 0.0e0
allele num: 11546
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10374
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Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66598
num of homozygotes: 0

East Asian
type: Population
allele count: 6
allele frequency: 6.949270326615705e-4
allele num: 8634
num of homozygotes: 0

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

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16456
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 1.253e0

MQRankSum
type: SiteQuality
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MQ
type: SiteQuality
SIO_000300: 5.968e1

BaseQRankSum
type: SiteQuality
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QD
type: SiteQuality
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VQSLOD
type: SiteQuality
SIO_000300: 2.51e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.0e-4

ReadPosRankSum
type: SiteQuality
SIO_000300: 9.409999999999999e-1

DP
type: SiteQuality
SIO_000300: 1.72249e6

ClippingRankSum
type: SiteQuality
SIO_000300: -7.76e-1

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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variant carriers: 0

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

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66568
num of homozygotes: 0

East Asian
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allele count: 3
allele frequency: 3.476245654692932e-4
allele num: 8630
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Other
type: Population
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allele frequency: 0.0e0
allele num: 906
num of homozygotes: 0

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

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11540
num of homozygotes: 0

VQSLOD
type: SiteQuality
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FS
type: SiteQuality
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QD
type: SiteQuality
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MQRankSum
type: SiteQuality
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InbreedingCoeff
type: SiteQuality
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ClippingRankSum
type: SiteQuality
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DP
type: SiteQuality
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ReadPosRankSum
type: SiteQuality
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MQ
type: SiteQuality
SIO_000300: 5.965e1

BaseQRankSum
type: SiteQuality
SIO_000300: -3.163e0

GenotypeQuality
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variant carriers: 3

GenotypeQuality
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GenotypeQuality
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bin: 7.75e1
variant carriers: 0

Latino
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allele frequency: 8.668515950069348e-5
allele num: 11536
num of homozygotes: 0

European (Finnish)
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allele frequency: 0.0e0
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South Asian
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European (Non-Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 66556
num of homozygotes: 0

African
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allele frequency: 1.92975685063682e-4
allele num: 10364
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East Asian
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Other
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num of homozygotes: 0

QD
type: SiteQuality
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InbreedingCoeff
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FS
type: SiteQuality
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MQRankSum
type: SiteQuality
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ClippingRankSum
type: SiteQuality
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MQ
type: SiteQuality
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ReadPosRankSum
type: SiteQuality
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BaseQRankSum
type: SiteQuality
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DP
type: SiteQuality
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VQSLOD
type: SiteQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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bin: 8.25e1
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Other
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allele num: 904
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African
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allele frequency: 1.93012931866435e-4
allele num: 10362
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European (Finnish)
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East Asian
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European (Non-Finnish)
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allele frequency: 1.052030418708107e-4
allele num: 66538
num of homozygotes: 0

Latino
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allele frequency: 8.668515950069348e-5
allele num: 11536
num of homozygotes: 0

South Asian
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FS
type: SiteQuality
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MQRankSum
type: SiteQuality
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ClippingRankSum
type: SiteQuality
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MQ
type: SiteQuality
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ReadPosRankSum
type: SiteQuality
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BaseQRankSum
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VQSLOD
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InbreedingCoeff
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DP
type: SiteQuality
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QD
type: SiteQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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European (Finnish)
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allele num: 6608
num of homozygotes: 0

South Asian
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Latino
type: Population
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East Asian
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African
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European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
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Other
type: Population
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InbreedingCoeff
type: SiteQuality
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FS
type: SiteQuality
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BaseQRankSum
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MQ
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ClippingRankSum
type: SiteQuality
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MQRankSum
type: SiteQuality
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VQSLOD
type: SiteQuality
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QD
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DP
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ReadPosRankSum
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

South Asian
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European (Non-Finnish)
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allele count: 1
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allele num: 66450
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African
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Latino
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allele count: 0
allele frequency: 0.0e0
allele num: 11526
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European (Finnish)
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allele frequency: 0.0e0
allele num: 6606
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East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
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Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 902
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 5.188e0

BaseQRankSum
type: SiteQuality
SIO_000300: -2.107e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.24e0

MQ
type: SiteQuality
SIO_000300: 5.961e1

VQSLOD
type: SiteQuality
SIO_000300: 8.3e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -1.94e0

MQRankSum
type: SiteQuality
SIO_000300: 5.25e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.0e-4

QD
type: SiteQuality
SIO_000300: 1.184e1

DP
type: SiteQuality
SIO_000300: 1.71082e6

GenotypeQuality
all individuals: 58
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1476
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2341
bin: 7.25e1
variant carriers: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 900
num of homozygotes: 0

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

African
type: Population
allele count: 1
allele frequency: 9.688044952528579e-5
allele num: 10322
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8612
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66400
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11520
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6602
num of homozygotes: 0

QD
type: SiteQuality
SIO_000300: 1.063e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.0e-4

MQRankSum
type: SiteQuality
SIO_000300: 1.42e0

VQSLOD
type: SiteQuality
SIO_000300: 8.179999999999999e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.75e0

ClippingRankSum
type: SiteQuality
SIO_000300: 7.17e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -1.547e0

DP
type: SiteQuality
SIO_000300: 1.706469e6

MQ
type: SiteQuality
SIO_000300: 5.961e1

FS
type: SiteQuality
SIO_000300: 0.0e0

GenotypeQuality
all individuals: 133
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 40238
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 559
bin: 8.75e1
variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8576
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 896
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6588
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 9.737098344693281e-5
allele num: 10270
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66170
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16328
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11468
num of homozygotes: 0

MQRankSum
type: SiteQuality
SIO_000300: -1.139e0

FS
type: SiteQuality
SIO_000300: 2.379e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 3.0e-4

MQ
type: SiteQuality
SIO_000300: 6.0e1

BaseQRankSum
type: SiteQuality
SIO_000300: -5.73e-1

VQSLOD
type: SiteQuality
SIO_000300: -2.365e-1

DP
type: SiteQuality
SIO_000300: 1.682109e6

QD
type: SiteQuality
SIO_000300: 9.02e0

ClippingRankSum
type: SiteQuality
SIO_000300: -1.139e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 9.64e-1

GenotypeQuality
all individuals: 2365
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 38789
bin: 6.25e1
variant carriers: 0

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

African
type: Population
allele count: 5
allele frequency: 4.894283476898982e-4
allele num: 10216
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8550
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 896
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11422
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6580
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16276
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 65880
num of homozygotes: 0

MQRankSum
type: SiteQuality
SIO_000300: 3.61e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 1.52e-1

DP
type: SiteQuality
SIO_000300: 1.648458e6

BaseQRankSum
type: SiteQuality
SIO_000300: -2.706e0

QD
type: SiteQuality
SIO_000300: 1.128e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.0e-4

VQSLOD
type: SiteQuality
SIO_000300: 1.5e0

FS
type: SiteQuality
SIO_000300: 6.865e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 8.500000000000001e-2

GenotypeQuality
all individuals: 19
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 537
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 691
bin: 9.25e1
variant carriers: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11402
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 65856
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 896
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10212
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16264
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6580
num of homozygotes: 0

East Asian
type: Population
allele count: 3
allele frequency: 3.512058066026691e-4
allele num: 8542
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 8.52e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 6.1e-1

MQRankSum
type: SiteQuality
SIO_000300: 9.85e-1

VQSLOD
type: SiteQuality
SIO_000300: 9.06e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 5.4e-2

MQ
type: SiteQuality
SIO_000300: 5.951e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.0e-4

BaseQRankSum
type: SiteQuality
SIO_000300: 1.41e0

QD
type: SiteQuality
SIO_000300: 1.39e1

DP
type: SiteQuality
SIO_000300: 1.639243e6

GenotypeQuality
all individuals: 1965
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 1262
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1945
bin: 7.25e1
variant carriers: 0

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

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 65744
num of homozygotes: 0

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

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16224
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 894
num of homozygotes: 0

East Asian
type: Population
allele count: 2
allele frequency: 2.34796900680911e-4
allele num: 8518
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10194
num of homozygotes: 0

MQ
type: SiteQuality
SIO_000300: 6.0e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.0e-4

VQSLOD
type: SiteQuality
SIO_000300: 1.27e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -2.516e0

MQRankSum
type: SiteQuality
SIO_000300: -1.174e0

QD
type: SiteQuality
SIO_000300: 1.021e1

FS
type: SiteQuality
SIO_000300: 2.604e0

ClippingRankSum
type: SiteQuality
SIO_000300: 5.03e-1

DP
type: SiteQuality
SIO_000300: 1.622229e6

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.94e-1

GenotypeQuality
all individuals: 1961
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 902
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 36436
bin: 6.25e1
variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8504
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 9.817396426467701e-5
allele num: 10186
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6568
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16224
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 65708
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 894
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11402
num of homozygotes: 0

MQ
type: SiteQuality
SIO_000300: 5.956e1

ClippingRankSum
type: SiteQuality
SIO_000300: 1.64e-1

FS
type: SiteQuality
SIO_000300: 1.21e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 8.97e-1

MQRankSum
type: SiteQuality
SIO_000300: 4.28e-1

QD
type: SiteQuality
SIO_000300: 1.173e1

VQSLOD
type: SiteQuality
SIO_000300: 2.14e0

DP
type: SiteQuality
SIO_000300: 1.609346e6

BaseQRankSum
type: SiteQuality
SIO_000300: -2.415e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.2e-3

GenotypeQuality
all individuals: 7002
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3713
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1961
bin: 9.75e1
variant carriers: 2

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 894
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10186
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6568
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11402
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16224
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8504
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 2
allele frequency: 3.043769404029951e-5
allele num: 65708
num of homozygotes: 0

ReadPosRankSum
type: SiteQuality
SIO_000300: 8.97e-1

FS
type: SiteQuality
SIO_000300: 1.21e0

BaseQRankSum
type: SiteQuality
SIO_000300: -2.415e0

MQ
type: SiteQuality
SIO_000300: 5.956e1

MQRankSum
type: SiteQuality
SIO_000300: 4.28e-1

DP
type: SiteQuality
SIO_000300: 1.609346e6

ClippingRankSum
type: SiteQuality
SIO_000300: 1.64e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.2e-3

VQSLOD
type: SiteQuality
SIO_000300: 2.14e0

QD
type: SiteQuality
SIO_000300: 1.173e1

GenotypeQuality
all individuals: 1618
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3425
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1927
bin: 9.75e1
variant carriers: 1

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

Latino
type: Population
allele count: 1
allele frequency: 9.057971014492754e-5
allele num: 11040
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6472
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 15866
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 63876
num of homozygotes: 0

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

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9954
num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: 5.21e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.6e-3

QD
type: SiteQuality
SIO_000300: 1.471e1

MQ
type: SiteQuality
SIO_000300: 6.0e1

DP
type: SiteQuality
SIO_000300: 1.354917e6

MQRankSum
type: SiteQuality
SIO_000300: 3.67e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 6.12e-1

FS
type: SiteQuality
SIO_000300: 0.0e0

ClippingRankSum
type: SiteQuality
SIO_000300: -1.511e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 4.49e-1

GenotypeQuality
all individuals: 354
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 4136
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 21703
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 5465
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 2667
bin: 8.75e1
variant carriers: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11556
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8636
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10392
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16194
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.504030802550836e-5
allele num: 66488
num of homozygotes: 0

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

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

BaseQRankSum
type: SiteQuality
SIO_000300: -3.326e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

FS
type: SiteQuality
SIO_000300: 5.493e0

DP
type: SiteQuality
SIO_000300: 2.264925e6

ReadPosRankSum
type: SiteQuality
SIO_000300: -8.1e-2

QD
type: SiteQuality
SIO_000300: 5.99e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.0e-4

ClippingRankSum
type: SiteQuality
SIO_000300: -1.6e-2

VQSLOD
type: SiteQuality
SIO_000300: -1.191e0

MQRankSum
type: SiteQuality
SIO_000300: 7.95e-1

GenotypeQuality
all individuals: 4108
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 167
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 2650
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 5608
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3159
bin: 7.25e1
variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8642
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10402
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11564
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66524
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16266
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 1
allele frequency: 1.51285930408472e-4
allele num: 6610
num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: 9.2e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

MQRankSum
type: SiteQuality
SIO_000300: 8.6e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -7.42e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -1.24e0

DP
type: SiteQuality
SIO_000300: 2.282183e6

InbreedingCoeff
type: SiteQuality
SIO_000300: 5.6e-3

FS
type: SiteQuality
SIO_000300: 3.024e0

QD
type: SiteQuality
SIO_000300: 1.319e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.18e0

GenotypeQuality
all individuals: 4904
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 11601
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 157
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 374
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 5613
bin: 6.75e1
variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8644
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16272
num of homozygotes: 0

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

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11562
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10402
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.503216884132043e-5
allele num: 66524
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

ReadPosRankSum
type: SiteQuality
SIO_000300: 9.02e-1

DP
type: SiteQuality
SIO_000300: 2.28416e6

BaseQRankSum
type: SiteQuality
SIO_000300: 1.06e0

MQRankSum
type: SiteQuality
SIO_000300: 1.66e0

MQ
type: SiteQuality
SIO_000300: 5.898e1

InbreedingCoeff
type: SiteQuality
SIO_000300: 6.6e-3

VQSLOD
type: SiteQuality
SIO_000300: 2.96e-1

FS
type: SiteQuality
SIO_000300: 1.385e0

QD
type: SiteQuality
SIO_000300: 1.472e1

ClippingRankSum
type: SiteQuality
SIO_000300: -8.76e-1

GenotypeQuality
all individuals: 5670
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 217
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 21701
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 2667
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 4934
bin: 7.75e1
variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8646
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 1
allele frequency: 1.513775355737209e-4
allele num: 6606
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11564
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10400
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66534
num of homozygotes: 0

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

VQSLOD
type: SiteQuality
SIO_000300: 3.0e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 4.0e-4

MQ
type: SiteQuality
SIO_000300: 6.0e1

QD
type: SiteQuality
SIO_000300: 1.685e1

MQRankSum
type: SiteQuality
SIO_000300: 5.13e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -2.442e0

BaseQRankSum
type: SiteQuality
SIO_000300: -3.347e0

DP
type: SiteQuality
SIO_000300: 2.290831e6

FS
type: SiteQuality
SIO_000300: 0.0e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.91e-1

GenotypeQuality
all individuals: 152
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 21703
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variant carriers: 1

GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 4742
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GenotypeQuality
all individuals: 12176
bin: 6.25e1
variant carriers: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

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

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8648
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.502584445245823e-5
allele num: 66552
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11564
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16324
num of homozygotes: 0

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

BaseQRankSum
type: SiteQuality
SIO_000300: 2.08e0

VQSLOD
type: SiteQuality
SIO_000300: 5.03e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -1.149e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 5.7e-3

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.24e0

MQRankSum
type: SiteQuality
SIO_000300: -2.39e-1

FS
type: SiteQuality
SIO_000300: 3.289e0

QD
type: SiteQuality
SIO_000300: 1.239e1

DP
type: SiteQuality
SIO_000300: 2.29576e6

MQ
type: SiteQuality
SIO_000300: 5.917e1

GenotypeQuality
all individuals: 12443
bin: 6.25e1
variant carriers: 0

GenotypeQuality
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GenotypeQuality
all individuals: 21702
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GenotypeQuality
all individuals: 88
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 101
bin: 4.75e1
variant carriers: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66562
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

Latino
type: Population
allele count: 1
allele frequency: 8.647526807333103e-5
allele num: 11564
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16354
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10402
num of homozygotes: 0

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

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8648
num of homozygotes: 0

ReadPosRankSum
type: SiteQuality
SIO_000300: 2.0e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

VQSLOD
type: SiteQuality
SIO_000300: 7.23e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 3.01e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 7.0e-3

FS
type: SiteQuality
SIO_000300: 2.103e0

QD
type: SiteQuality
SIO_000300: 8.98e0

ClippingRankSum
type: SiteQuality
SIO_000300: 1.34e-1

MQRankSum
type: SiteQuality
SIO_000300: 6.7e-2

DP
type: SiteQuality
SIO_000300: 2.297202e6

GenotypeQuality
all individuals: 21702
bin: 9.75e1
variant carriers: 1

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
all individuals: 70
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GenotypeQuality
all individuals: 235
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variant carriers: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16358
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.502403846153846e-5
allele num: 66560
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11564
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8648
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10404
num of homozygotes: 0

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

VQSLOD
type: SiteQuality
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QD
type: SiteQuality
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ClippingRankSum
type: SiteQuality
SIO_000300: -1.394e0

FS
type: SiteQuality
SIO_000300: 2.607e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 2.05e0

MQRankSum
type: SiteQuality
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InbreedingCoeff
type: SiteQuality
SIO_000300: 5.0e-4

BaseQRankSum
type: SiteQuality
SIO_000300: 3.32e0

DP
type: SiteQuality
SIO_000300: 2.29841e6

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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bin: 6.75e1
variant carriers: 0

Latino
type: Population
allele count: 1
allele frequency: 8.646031471554557e-5
allele num: 11566
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8648
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

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

African
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allele count: 0
allele frequency: 0.0e0
allele num: 10404
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66614
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16430
num of homozygotes: 0

BaseQRankSum
type: SiteQuality
SIO_000300: 1.91e0

MQRankSum
type: SiteQuality
SIO_000300: 1.63e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

VQSLOD
type: SiteQuality
SIO_000300: -2.616e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 3.2e-3

ClippingRankSum
type: SiteQuality
SIO_000300: -6.6e-2

QD
type: SiteQuality
SIO_000300: 2.19e0

FS
type: SiteQuality
SIO_000300: 1.1899e1

DP
type: SiteQuality
SIO_000300: 2.303517e6

ReadPosRankSum
type: SiteQuality
SIO_000300: -2.48e-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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South Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 16444
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8650
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66624
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

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

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10404
num of homozygotes: 0

Latino
type: Population
allele count: 1
allele frequency: 8.646031471554557e-5
allele num: 11566
num of homozygotes: 0

MQRankSum
type: SiteQuality
SIO_000300: 7.8e-1

VQSLOD
type: SiteQuality
SIO_000300: -5.12e-2

DP
type: SiteQuality
SIO_000300: 2.30418e6

InbreedingCoeff
type: SiteQuality
SIO_000300: 3.9e-3

QD
type: SiteQuality
SIO_000300: 1.151e1

ClippingRankSum
type: SiteQuality
SIO_000300: 1.51e0

MQ
type: SiteQuality
SIO_000300: 5.936e1

FS
type: SiteQuality
SIO_000300: 0.0e0

BaseQRankSum
type: SiteQuality
SIO_000300: 1.32e0

ReadPosRankSum
type: SiteQuality
SIO_000300: -1.206e0

GenotypeQuality
all individuals: 3
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 3216
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GenotypeQuality
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variant carriers: 3

GenotypeQuality
all individuals: 4126
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GenotypeQuality
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bin: 8.75e1
variant carriers: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16444
num of homozygotes: 0

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

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66626
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11566
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8648
num of homozygotes: 0

African
type: Population
allele count: 3
allele frequency: 2.883506343713956e-4
allele num: 10404
num of homozygotes: 0

MQRankSum
type: SiteQuality
SIO_000300: -6.8e-2

ReadPosRankSum
type: SiteQuality
SIO_000300: -1.88e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 2.7e-3

VQSLOD
type: SiteQuality
SIO_000300: 1.48e0

FS
type: SiteQuality
SIO_000300: 5.454e0

MQ
type: SiteQuality
SIO_000300: 5.961e1

DP
type: SiteQuality
SIO_000300: 2.304438e6

BaseQRankSum
type: SiteQuality
SIO_000300: -2.822e0

QD
type: SiteQuality
SIO_000300: 1.448e1

ClippingRankSum
type: SiteQuality
SIO_000300: 2.35e-1

GenotypeQuality
all individuals: 21707
bin: 9.75e1
variant carriers: 3

GenotypeQuality
all individuals: 29
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variant carriers: 0

GenotypeQuality
all individuals: 15
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variant carriers: 0

GenotypeQuality
all individuals: 32
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variant carriers: 0

GenotypeQuality
all individuals: 4763
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GenotypeQuality
all individuals: 3219
bin: 7.25e1
variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8654
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11566
num of homozygotes: 0

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

African
type: Population
allele count: 1
allele frequency: 9.611687812379854e-5
allele num: 10404
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16466
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 2
allele frequency: 3.000930288389401e-5
allele num: 66646
num of homozygotes: 0

DP
type: SiteQuality
SIO_000300: 2.306088e6

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.0e-4

BaseQRankSum
type: SiteQuality
SIO_000300: -2.083e0

QD
type: SiteQuality
SIO_000300: 1.141e1

ClippingRankSum
type: SiteQuality
SIO_000300: 3.3e-2

VQSLOD
type: SiteQuality
SIO_000300: 1.69e0

MQRankSum
type: SiteQuality
SIO_000300: 6.34e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 3.6e-2

FS
type: SiteQuality
SIO_000300: 1.314e0

GenotypeQuality
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bin: 7.25e1
variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 1

GenotypeQuality
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variant carriers: 0

African
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allele count: 0
allele frequency: 0.0e0
allele num: 10404
num of homozygotes: 0

Other
type: Population
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allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

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

East Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 8654
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.500060002400096e-5
allele num: 66664
num of homozygotes: 0

South Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 16490
num of homozygotes: 0

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

ClippingRankSum
type: SiteQuality
SIO_000300: 1.0e0

BaseQRankSum
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DP
type: SiteQuality
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QD
type: SiteQuality
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FS
type: SiteQuality
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InbreedingCoeff
type: SiteQuality
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ReadPosRankSum
type: SiteQuality
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VQSLOD
type: SiteQuality
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MQ
type: SiteQuality
SIO_000300: 6.0e1

MQRankSum
type: SiteQuality
SIO_000300: 3.1e-2

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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bin: 6.25e1
variant carriers: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.49902563333833e-5
allele num: 66710
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

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

African
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allele num: 10404
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South Asian
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allele frequency: 0.0e0
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East Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 8654
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11574
num of homozygotes: 0

InbreedingCoeff
type: SiteQuality
SIO_000300: 8.500000000000001e-3

DP
type: SiteQuality
SIO_000300: 2.308946e6

BaseQRankSum
type: SiteQuality
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VQSLOD
type: SiteQuality
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MQRankSum
type: SiteQuality
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MQ
type: SiteQuality
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FS
type: SiteQuality
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QD
type: SiteQuality
SIO_000300: 1.189e1

ClippingRankSum
type: SiteQuality
SIO_000300: -1.382e0

ReadPosRankSum
type: SiteQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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variant carriers: 3

GenotypeQuality
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variant carriers: 0

African
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allele count: 0
allele frequency: 0.0e0
allele num: 10404
num of homozygotes: 0

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

European (Non-Finnish)
type: Population
allele count: 2
allele frequency: 2.997691777331455e-5
allele num: 66718
num of homozygotes: 0

Other
type: Population
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allele num: 908
num of homozygotes: 0

East Asian
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allele count: 1
allele frequency: 1.155535012710885e-4
allele num: 8654
num of homozygotes: 0

South Asian
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allele frequency: 0.0e0
allele num: 16506
num of homozygotes: 0

Latino
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allele num: 11574
num of homozygotes: 0

ClippingRankSum
type: SiteQuality
SIO_000300: -8.53e-1

QD
type: SiteQuality
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DP
type: SiteQuality
SIO_000300: 2.309243e6

MQ
type: SiteQuality
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FS
type: SiteQuality
SIO_000300: 9.002000000000001e0

ReadPosRankSum
type: SiteQuality
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VQSLOD
type: SiteQuality
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BaseQRankSum
type: SiteQuality
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MQRankSum
type: SiteQuality
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InbreedingCoeff
type: SiteQuality
SIO_000300: -1.0e-4

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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bin: 9.75e1
variant carriers: 55

East Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 8654
num of homozygotes: 0

European (Non-Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 66726
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European (Finnish)
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allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

African
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allele frequency: 4.805843906189927e-3
allele num: 10404
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Other
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allele num: 908
num of homozygotes: 0

South Asian
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allele count: 0
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Latino
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allele count: 4
allele frequency: 3.456022118541559e-4
allele num: 11574
num of homozygotes: 0

QD
type: SiteQuality
SIO_000300: 1.315e1

BaseQRankSum
type: SiteQuality
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VQSLOD
type: SiteQuality
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MQRankSum
type: SiteQuality
SIO_000300: 1.39e-1

ClippingRankSum
type: SiteQuality
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FS
type: SiteQuality
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DP
type: SiteQuality
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MQ
type: SiteQuality
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InbreedingCoeff
type: SiteQuality
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ReadPosRankSum
type: SiteQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 19

GenotypeQuality
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bin: 6.25e1
variant carriers: 0

GenotypeQuality
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variant carriers: 0

European (Non-Finnish)
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allele frequency: 0.0e0
allele num: 66728
num of homozygotes: 0

Other
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allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

Latino
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allele count: 19
allele frequency: 1.64161050630724e-3
allele num: 11574
num of homozygotes: 0

South Asian
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allele frequency: 0.0e0
allele num: 16510
num of homozygotes: 0

African
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allele count: 0
allele frequency: 0.0e0
allele num: 10404
num of homozygotes: 0

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

East Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 8654
num of homozygotes: 0

QD
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MQ
type: SiteQuality
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InbreedingCoeff
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BaseQRankSum
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FS
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DP
type: SiteQuality
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VQSLOD
type: SiteQuality
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ReadPosRankSum
type: SiteQuality
SIO_000300: 4.99e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 2.67e-1

MQRankSum
type: SiteQuality
SIO_000300: 1.11e-1

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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bin: 1.75e1
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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bin: 2.75e1
variant carriers: 0

East Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 8654
num of homozygotes: 0

African
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allele count: 0
allele frequency: 0.0e0
allele num: 10404
num of homozygotes: 0

Latino
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allele frequency: 0.0e0
allele num: 11574
num of homozygotes: 0

European (Non-Finnish)
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allele count: 1
allele frequency: 1.498531439189594e-5
allele num: 66732
num of homozygotes: 0

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

South Asian
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allele frequency: 0.0e0
allele num: 16510
num of homozygotes: 0

Other
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allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

ClippingRankSum
type: SiteQuality
SIO_000300: -2.06e-1

InbreedingCoeff
type: SiteQuality
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BaseQRankSum
type: SiteQuality
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DP
type: SiteQuality
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VQSLOD
type: SiteQuality
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FS
type: SiteQuality
SIO_000300: 4.337e0

MQRankSum
type: SiteQuality
SIO_000300: -1.1e-2

QD
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MQ
type: SiteQuality
SIO_000300: 5.973e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 4.44e-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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variant carriers: 0

East Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 8654
num of homozygotes: 0

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

European (Non-Finnish)
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allele count: 2
allele frequency: 2.997062878379188e-5
allele num: 66732
num of homozygotes: 0

South Asian
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allele count: 84
allele frequency: 5.087825560266505e-3
allele num: 16510
num of homozygotes: 0

Other
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allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

African
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allele count: 0
allele frequency: 0.0e0
allele num: 10404
num of homozygotes: 0

Latino
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allele frequency: 8.640055296353897e-5
allele num: 11574
num of homozygotes: 0

BaseQRankSum
type: SiteQuality
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MQ
type: SiteQuality
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ClippingRankSum
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DP
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QD
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InbreedingCoeff
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ReadPosRankSum
type: SiteQuality
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MQRankSum
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VQSLOD
type: SiteQuality
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FS
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 1

Other
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allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

East Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 8654
num of homozygotes: 0

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

European (Non-Finnish)
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allele frequency: 0.0e0
allele num: 66734
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European (Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 6614
num of homozygotes: 0

African
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allele frequency: 0.0e0
allele num: 10404
num of homozygotes: 0

Latino
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allele frequency: 8.640055296353897e-5
allele num: 11574
num of homozygotes: 0

BaseQRankSum
type: SiteQuality
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MQ
type: SiteQuality
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DP
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FS
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InbreedingCoeff
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MQRankSum
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VQSLOD
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ReadPosRankSum
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ClippingRankSum
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QD
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GenotypeQuality
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GenotypeQuality
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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
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allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

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

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

European (Non-Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 66738
num of homozygotes: 0

Latino
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allele count: 0
allele frequency: 0.0e0
allele num: 11578
num of homozygotes: 0

South Asian
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allele frequency: 6.056201550387597e-5
allele num: 16512
num of homozygotes: 0

East Asian
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allele frequency: 0.0e0
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DP
type: SiteQuality
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MQRankSum
type: SiteQuality
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QD
type: SiteQuality
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FS
type: SiteQuality
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ReadPosRankSum
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BaseQRankSum
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VQSLOD
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ClippingRankSum
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MQ
type: SiteQuality
SIO_000300: 5.914e1

InbreedingCoeff
type: SiteQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

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

Latino
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allele count: 0
allele frequency: 0.0e0
allele num: 11578
num of homozygotes: 0

South Asian
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allele frequency: 6.056201550387597e-5
allele num: 16512
num of homozygotes: 0

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

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

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

European (Non-Finnish)
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allele count: 3
allele frequency: 4.495324862143371e-5
allele num: 66736
num of homozygotes: 0

MQ
type: SiteQuality
SIO_000300: 6.0e1

FS
type: SiteQuality
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ClippingRankSum
type: SiteQuality
SIO_000300: -5.2e-1

ReadPosRankSum
type: SiteQuality
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DP
type: SiteQuality
SIO_000300: 2.310683e6

MQRankSum
type: SiteQuality
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QD
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BaseQRankSum
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VQSLOD
type: SiteQuality
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InbreedingCoeff
type: SiteQuality
SIO_000300: 1.0e-4

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

Latino
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allele frequency: 0.0e0
allele num: 11578
num of homozygotes: 0

East Asian
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allele count: 0
allele frequency: 0.0e0
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Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10404
num of homozygotes: 0

European (Non-Finnish)
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allele count: 1
allele frequency: 1.498441620714457e-5
allele num: 66736
num of homozygotes: 0

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

MQRankSum
type: SiteQuality
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MQ
type: SiteQuality
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ReadPosRankSum
type: SiteQuality
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QD
type: SiteQuality
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InbreedingCoeff
type: SiteQuality
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ClippingRankSum
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BaseQRankSum
type: SiteQuality
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VQSLOD
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FS
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DP
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GenotypeQuality
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variant carriers: 2

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

European (Non-Finnish)
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allele frequency: 2.996973057212216e-5
allele num: 66734
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Other
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East Asian
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African
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South Asian
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European (Finnish)
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allele frequency: 0.0e0
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MQRankSum
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BaseQRankSum
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FS
type: SiteQuality
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ReadPosRankSum
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QD
type: SiteQuality
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VQSLOD
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MQ
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InbreedingCoeff
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DP
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ClippingRankSum
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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Other
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European (Finnish)
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Latino
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European (Non-Finnish)
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allele num: 66734
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East Asian
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African
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South Asian
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FS
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DP
type: SiteQuality
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MQRankSum
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QD
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BaseQRankSum
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VQSLOD
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ReadPosRankSum
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InbreedingCoeff
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MQ
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ClippingRankSum
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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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East Asian
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European (Non-Finnish)
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Latino
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African
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European (Finnish)
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South Asian
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Other
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InbreedingCoeff
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ClippingRankSum
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DP
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FS
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MQ
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MQRankSum
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BaseQRankSum
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VQSLOD
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QD
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ReadPosRankSum
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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Latino
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European (Non-Finnish)
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African
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South Asian
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East Asian
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Other
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European (Finnish)
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VQSLOD
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DP
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BaseQRankSum
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ReadPosRankSum
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QD
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FS
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InbreedingCoeff
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MQRankSum
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ClippingRankSum
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MQ
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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European (Finnish)
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num of homozygotes: 0

African
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allele frequency: 0.0e0
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num of homozygotes: 0

Latino
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allele frequency: 0.0e0
allele num: 11576
num of homozygotes: 0

European (Non-Finnish)
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allele count: 1
allele frequency: 1.498756032493031e-5
allele num: 66722
num of homozygotes: 0

Other
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allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

South Asian
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allele frequency: 0.0e0
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East Asian
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allele frequency: 0.0e0
allele num: 8654
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 8.29e-1

QD
type: SiteQuality
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MQRankSum
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VQSLOD
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InbreedingCoeff
type: SiteQuality
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DP
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ReadPosRankSum
type: SiteQuality
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ClippingRankSum
type: SiteQuality
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BaseQRankSum
type: SiteQuality
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MQ
type: SiteQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

African
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allele frequency: 0.0e0
allele num: 10402
num of homozygotes: 0

European (Non-Finnish)
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allele frequency: 0.0e0
allele num: 66714
num of homozygotes: 0

East Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 8654
num of homozygotes: 0

South Asian
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allele count: 1
allele frequency: 6.05913717886573e-5
allele num: 16504
num of homozygotes: 0

Other
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allele count: 0
allele frequency: 0.0e0
allele num: 906
num of homozygotes: 0

Latino
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allele count: 0
allele frequency: 0.0e0
allele num: 11576
num of homozygotes: 0

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

VQSLOD
type: SiteQuality
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ReadPosRankSum
type: SiteQuality
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FS
type: SiteQuality
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DP
type: SiteQuality
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MQRankSum
type: SiteQuality
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InbreedingCoeff
type: SiteQuality
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ClippingRankSum
type: SiteQuality
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MQ
type: SiteQuality
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QD
type: SiteQuality
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BaseQRankSum
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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variant carriers: 0

South Asian
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allele count: 1
allele frequency: 6.06060606060606e-5
allele num: 16500
num of homozygotes: 0

East Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 8654
num of homozygotes: 0

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

Latino
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allele frequency: 0.0e0
allele num: 11576
num of homozygotes: 0

Other
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allele count: 0
allele frequency: 0.0e0
allele num: 906
num of homozygotes: 0

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

InbreedingCoeff
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ClippingRankSum
type: SiteQuality
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VQSLOD
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MQRankSum
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DP
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QD
type: SiteQuality
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MQ
type: SiteQuality
SIO_000300: 5.928e1

ReadPosRankSum
type: SiteQuality
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FS
type: SiteQuality
SIO_000300: 4.26e0

BaseQRankSum
type: SiteQuality
SIO_000300: -9.54e-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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Other
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allele count: 0
allele frequency: 0.0e0
allele num: 906
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
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Latino
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allele frequency: 0.0e0
allele num: 11576
num of homozygotes: 0

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

European (Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 6614
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European (Non-Finnish)
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allele count: 1
allele frequency: 1.499835018148004e-5
allele num: 66674
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African
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allele count: 0
allele frequency: 0.0e0
allele num: 10388
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 3.867e0

ClippingRankSum
type: SiteQuality
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VQSLOD
type: SiteQuality
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QD
type: SiteQuality
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InbreedingCoeff
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MQ
type: SiteQuality
SIO_000300: 5.79e1

ReadPosRankSum
type: SiteQuality
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MQRankSum
type: SiteQuality
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BaseQRankSum
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DP
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SIO_000300: 2.305566e6

GenotypeQuality
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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)
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allele count: 0
allele frequency: 0.0e0
allele num: 66614
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6612
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Latino
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allele count: 0
allele frequency: 0.0e0
allele num: 11570
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African
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allele count: 1
allele frequency: 9.632055480639569e-5
allele num: 10382
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8650
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Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 904
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South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16402
num of homozygotes: 0

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.68e-2

ReadPosRankSum
type: SiteQuality
SIO_000300: -8.47e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -2.916e0

FS
type: SiteQuality
SIO_000300: 0.0e0

ClippingRankSum
type: SiteQuality
SIO_000300: 1.25e0

DP
type: SiteQuality
SIO_000300: 2.28831e6

MQRankSum
type: SiteQuality
SIO_000300: -8.0e-2

VQSLOD
type: SiteQuality
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MQ
type: SiteQuality
SIO_000300: 5.864e1

QD
type: SiteQuality
SIO_000300: 1.584e1

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

Latino
type: Population
allele count: 1
allele frequency: 8.64902266043937e-5
allele num: 11562
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6610
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European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66602
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African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10382
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Other
type: Population
allele count: 0
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allele num: 902
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South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
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East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8648
num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: -4.341e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 9.599999999999999e-3

ReadPosRankSum
type: SiteQuality
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DP
type: SiteQuality
SIO_000300: 2.276592e6

BaseQRankSum
type: SiteQuality
SIO_000300: -3.461e0

FS
type: SiteQuality
SIO_000300: 4.087e0

MQ
type: SiteQuality
SIO_000300: 6.0e1

ClippingRankSum
type: SiteQuality
SIO_000300: -6.55e-1

MQRankSum
type: SiteQuality
SIO_000300: -1.2e-1

QD
type: SiteQuality
SIO_000300: 1.833e1

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

European (Non-Finnish)
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allele count: 1
allele frequency: 1.504890895410083e-5
allele num: 66450
num of homozygotes: 0

Other
type: Population
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allele num: 898
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European (Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 6602
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South Asian
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allele frequency: 0.0e0
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East Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 8588
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Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11546
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 9.735202492211838e-5
allele num: 10272
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MQRankSum
type: SiteQuality
SIO_000300: 8.92e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 4.0e-4

ClippingRankSum
type: SiteQuality
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FS
type: SiteQuality
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QD
type: SiteQuality
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ReadPosRankSum
type: SiteQuality
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BaseQRankSum
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VQSLOD
type: SiteQuality
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MQ
type: SiteQuality
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DP
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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Other
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allele num: 898
num of homozygotes: 0

South Asian
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African
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allele frequency: 1.946661475569399e-4
allele num: 10274
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European (Non-Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 66492
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Latino
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allele count: 1
allele frequency: 8.661008141347653e-5
allele num: 11546
num of homozygotes: 0

East Asian
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allele num: 8596
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European (Finnish)
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allele frequency: 0.0e0
allele num: 6602
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VQSLOD
type: SiteQuality
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DP
type: SiteQuality
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InbreedingCoeff
type: SiteQuality
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BaseQRankSum
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MQRankSum
type: SiteQuality
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FS
type: SiteQuality
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ClippingRankSum
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ReadPosRankSum
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QD
type: SiteQuality
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MQ
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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variant carriers: 1

European (Finnish)
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allele frequency: 0.0e0
allele num: 6602
num of homozygotes: 0

African
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South Asian
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European (Non-Finnish)
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allele frequency: 1.503668952243474e-5
allele num: 66504
num of homozygotes: 0

East Asian
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Other
type: Population
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Latino
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ReadPosRankSum
type: SiteQuality
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FS
type: SiteQuality
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ClippingRankSum
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VQSLOD
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InbreedingCoeff
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BaseQRankSum
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MQ
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QD
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MQRankSum
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DP
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GenotypeQuality
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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

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

African
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allele frequency: 0.0e0
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European (Non-Finnish)
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European (Finnish)
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East Asian
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allele frequency: 4.645760743321719e-4
allele num: 8610
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Other
type: Population
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South Asian
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MQRankSum
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BaseQRankSum
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ReadPosRankSum
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InbreedingCoeff
type: SiteQuality
SIO_000300: 1.0e-4

FS
type: SiteQuality
SIO_000300: 6.55e-1

QD
type: SiteQuality
SIO_000300: 1.328e1

MQ
type: SiteQuality
SIO_000300: 5.967e1

VQSLOD
type: SiteQuality
SIO_000300: 1.95e0

DP
type: SiteQuality
SIO_000300: 1.984037e6

ClippingRankSum
type: SiteQuality
SIO_000300: -5.51e-1

GenotypeQuality
all individuals: 1
bin: 2.5e0
variant carriers: 0

GenotypeQuality
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bin: 1.25e1
variant carriers: 0

GenotypeQuality
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bin: 9.75e1
variant carriers: 3

GenotypeQuality
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bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 8546
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3713
bin: 7.25e1
variant carriers: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11562
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8628
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10324
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6604
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 3
allele frequency: 4.499370088187654e-5
allele num: 66676
num of homozygotes: 0

South Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 16492
num of homozygotes: 0

InbreedingCoeff
type: SiteQuality
SIO_000300: 2.0e-4

ClippingRankSum
type: SiteQuality
SIO_000300: -2.12e-1

FS
type: SiteQuality
SIO_000300: 1.199e0

DP
type: SiteQuality
SIO_000300: 1.989143e6

BaseQRankSum
type: SiteQuality
SIO_000300: 4.62e0

MQRankSum
type: SiteQuality
SIO_000300: 1.62e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 6.35e-1

VQSLOD
type: SiteQuality
SIO_000300: 3.66e0

MQ
type: SiteQuality
SIO_000300: 5.964e1

QD
type: SiteQuality
SIO_000300: 1.145e1

GenotypeQuality
all individuals: 1
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 2713
bin: 9.25e1
variant carriers: 0

GenotypeQuality
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bin: 2.75e1
variant carriers: 0

GenotypeQuality
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bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 10601
bin: 9.75e1
variant carriers: 4

GenotypeQuality
all individuals: 6
bin: 5.25e1
variant carriers: 0

African
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allele count: 1
allele frequency: 9.686168151879117e-5
allele num: 10324
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11562
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6604
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16492
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8628
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 3
allele frequency: 4.499370088187654e-5
allele num: 66676
num of homozygotes: 0

MQRankSum
type: SiteQuality
SIO_000300: 1.62e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 4.62e0

DP
type: SiteQuality
SIO_000300: 1.989143e6

ClippingRankSum
type: SiteQuality
SIO_000300: -2.12e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 6.35e-1

VQSLOD
type: SiteQuality
SIO_000300: 3.66e0

FS
type: SiteQuality
SIO_000300: 1.199e0

QD
type: SiteQuality
SIO_000300: 1.145e1

InbreedingCoeff
type: SiteQuality
SIO_000300: 2.0e-4

MQ
type: SiteQuality
SIO_000300: 5.964e1

GenotypeQuality
all individuals: 3
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 30
bin: 3.25e1
variant carriers: 0

GenotypeQuality
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bin: 6.25e1
variant carriers: 0

GenotypeQuality
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bin: 9.75e1
variant carriers: 2

GenotypeQuality
all individuals: 3713
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1852
bin: 8.75e1
variant carriers: 0

East Asian
type: Population
allele count: 2
allele frequency: 2.318034306907742e-4
allele num: 8628
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16496
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11562
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6604
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10330
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66678
num of homozygotes: 0

QD
type: SiteQuality
SIO_000300: 1.028e1

ClippingRankSum
type: SiteQuality
SIO_000300: 3.24e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 5.35e-2

DP
type: SiteQuality
SIO_000300: 1.988948e6

MQRankSum
type: SiteQuality
SIO_000300: -5.0e-2

VQSLOD
type: SiteQuality
SIO_000300: 2.4e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 3.09e-1

MQ
type: SiteQuality
SIO_000300: 5.944e1

FS
type: SiteQuality
SIO_000300: 0.0e0

BaseQRankSum
type: SiteQuality
SIO_000300: -1.656e0

GenotypeQuality
all individuals: 1852
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 2712
bin: 9.25e1
variant carriers: 0

GenotypeQuality
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bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 23878
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 10592
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 3714
bin: 7.25e1
variant carriers: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8630
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10334
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.499655079331754e-5
allele num: 66682
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16498
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6604
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11562
num of homozygotes: 0

ReadPosRankSum
type: SiteQuality
SIO_000300: 4.44e-1

FS
type: SiteQuality
SIO_000300: 5.23e-1

MQRankSum
type: SiteQuality
SIO_000300: 2.13e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -1.052e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 0.0e0

QD
type: SiteQuality
SIO_000300: 1.013e1

VQSLOD
type: SiteQuality
SIO_000300: 2.93e0

MQ
type: SiteQuality
SIO_000300: 5.966e1

DP
type: SiteQuality
SIO_000300: 1.989097e6

ClippingRankSum
type: SiteQuality
SIO_000300: 1.44e0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 20
bin: 5.25e1
variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 6
bin: 4.75e1
variant carriers: 0

GenotypeQuality
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bin: 8.75e1
variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8630
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6604
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.499610101373643e-5
allele num: 66684
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11562
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10334
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16500
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 3.501e0

VQSLOD
type: SiteQuality
SIO_000300: 3.17e-1

MQRankSum
type: SiteQuality
SIO_000300: -2.75e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 2.04e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: -1.98e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 0.0e0

MQ
type: SiteQuality
SIO_000300: 5.983e1

QD
type: SiteQuality
SIO_000300: 1.662e1

DP
type: SiteQuality
SIO_000300: 1.989164e6

BaseQRankSum
type: SiteQuality
SIO_000300: -1.355e0

GenotypeQuality
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bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 24
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variant carriers: 0

GenotypeQuality
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bin: 7.25e1
variant carriers: 0

GenotypeQuality
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bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 8547
bin: 6.75e1
variant carriers: 0

GenotypeQuality
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bin: 8.75e1
variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8628
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11562
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10336
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66682
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 6.06134076857801e-5
allele num: 16498
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6604
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.0e-4

MQRankSum
type: SiteQuality
SIO_000300: 4.21e-1

FS
type: SiteQuality
SIO_000300: 3.901e0

VQSLOD
type: SiteQuality
SIO_000300: 5.679999999999999e-1

QD
type: SiteQuality
SIO_000300: 9.630000000000001e0

ClippingRankSum
type: SiteQuality
SIO_000300: 1.31e0

MQ
type: SiteQuality
SIO_000300: 5.938e1

BaseQRankSum
type: SiteQuality
SIO_000300: -2.245e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 4.68e-1

DP
type: SiteQuality
SIO_000300: 1.98914e6

GenotypeQuality
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bin: 6.75e1
variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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bin: 3.25e1
variant carriers: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16496
num of homozygotes: 0

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

Latino
type: Population
allele count: 7
allele frequency: 6.050129645635263e-4
allele num: 11570
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10340
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8638
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.499430216517723e-5
allele num: 66692
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

DP
type: SiteQuality
SIO_000300: 1.989949e6

BaseQRankSum
type: SiteQuality
SIO_000300: 1.09e0

QD
type: SiteQuality
SIO_000300: 1.117e1

VQSLOD
type: SiteQuality
SIO_000300: 2.85e0

ClippingRankSum
type: SiteQuality
SIO_000300: 8.1e-2

MQ
type: SiteQuality
SIO_000300: 5.949e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 8.68e-1

MQRankSum
type: SiteQuality
SIO_000300: 1.18e-1

FS
type: SiteQuality
SIO_000300: 5.27e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.0e-4

GenotypeQuality
all individuals: 2712
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 85
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variant carriers: 0

GenotypeQuality
all individuals: 8542
bin: 6.75e1
variant carriers: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16498
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11570
num of homozygotes: 0

African
type: Population
allele count: 2
allele frequency: 1.933488012374323e-4
allele num: 10344
num of homozygotes: 0

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

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8638
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 3
allele frequency: 4.497885993583016e-5
allele num: 66698
num of homozygotes: 0

BaseQRankSum
type: SiteQuality
SIO_000300: -1.158e0

MQRankSum
type: SiteQuality
SIO_000300: 4.07e-1

InbreedingCoeff
type: SiteQuality
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QD
type: SiteQuality
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FS
type: SiteQuality
SIO_000300: 5.27e-1

VQSLOD
type: SiteQuality
SIO_000300: 2.57e0

MQ
type: SiteQuality
SIO_000300: 5.965e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.97e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 2.34e-1

DP
type: SiteQuality
SIO_000300: 1.989886e6

GenotypeQuality
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bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 10586
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 5103
bin: 7.75e1
variant carriers: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 908
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11566
num of homozygotes: 0

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

African
type: Population
allele count: 0
allele frequency: 0.0e0
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East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8638
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.499385252046661e-5
allele num: 66694
num of homozygotes: 0

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

VQSLOD
type: SiteQuality
SIO_000300: 6.11e-1

FS
type: SiteQuality
SIO_000300: 4.695e0

DP
type: SiteQuality
SIO_000300: 1.989302e6

ClippingRankSum
type: SiteQuality
SIO_000300: -5.36e-1

MQRankSum
type: SiteQuality
SIO_000300: -9.19e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 1.77e0

QD
type: SiteQuality
SIO_000300: 1.339e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.0e-4