3-25778867-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25778867
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25778867
    reference: chr 3
allele count: 2
allele frequency: 1.678021277309796e-5
allele num: 119188
alternate allele: A
annotation: Annotation
  canonical: true
  consequence: stop_gained
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.961C>T
  hgvsp: ENSP00000280700.5:p.Arg321Ter
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: stop_gained
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.961C>T
  hgvsp: ENSP00000379886.3:p.Arg321Ter
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: stop_gained
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.952C>T
  hgvsp: ENSP00000307980.5:p.Arg318Ter
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.712C>T
  hgvsp: ENST00000280699.9:c.712C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: stop_gained
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.961C>T
  hgvsp: ENSP00000387430.1:p.Arg321Ter
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.507C>T
  hgvsp: ENST00000422724.2:c.507C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.985C>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: stop_gained
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.835C>T
  hgvsp: ENSP00000389888.2:p.Arg279Ter
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: stop gained
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 365
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 306
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1075
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 289
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 480
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 422
  bin: 4.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 107
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11169
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 69
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 160
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 62
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 109
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 41943
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2855
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 77
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 263
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 197
  bin: 5.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 625
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 123
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 185
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 14
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 50538
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 192
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 18
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 332
  bin: 8.25e1
  variant carriers: 0
hgvs: p.Arg321Ter
num of homozygotes: 0
population: Latino
population: Other
population: European (Finnish)
population: European (Non-Finnish)
population: East Asian
population: African
population: South Asian
reference allele: G
site quality: ReadPosRankSum
site quality: QD
site quality: ClippingRankSum
site quality: MQRankSum
site quality: VQSLOD
site quality: FS
site quality: DP
site quality: MQ
site quality: InbreedingCoeff
site quality: BaseQRankSum

3-25778868-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25778868
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25778868
    reference: chr 3
allele count: 1
allele frequency: 8.38321345338095e-6
allele num: 119286
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.960C>T
  hgvsp: ENST00000428257.1:c.960C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.951C>T
  hgvsp: ENST00000308710.5:c.951C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.506C>T
  hgvsp: ENSP00000395878.2:p.Ala169Val
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.834C>T
  hgvsp: ENST00000417874.2:c.834C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.960C>T
  hgvsp: ENST00000396649.3:c.960C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.711C>T
  hgvsp: ENSP00000280699.9:p.Ala238Val
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.960C>T
  hgvsp: ENST00000280700.5:c.960C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.984C>T
  variant of: http://identifiers.org/hgnc/17646
canonical: false
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 423
  bin: 4.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 69
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 196
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 107
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2864
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 77
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 305
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 359
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11241
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 41941
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 289
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 262
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 458
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1033
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 123
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 109
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 619
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 159
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 62
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 169
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 604
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 189
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 156
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 16
  bin: 1.75e1
  variant carriers: 0
hgvs: p.Ala238Val
num of homozygotes: 0
population: African
population: Other
population: Latino
population: European (Non-Finnish)
population: South Asian
population: East Asian
population: European (Finnish)
reference allele: G
site quality: DP
site quality: BaseQRankSum
site quality: MQRankSum
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: MQ
site quality: ReadPosRankSum
site quality: FS
site quality: QD
site quality: VQSLOD

3-25778887-T-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25778887
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25778887
    reference: chr 3
allele count: 1
allele frequency: 8.308408109006315e-6
allele num: 120360
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.941A>G
  hgvsp: ENSP00000379886.3:p.Asn314Ser
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.965A>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.815A>G
  hgvsp: ENSP00000389888.2:p.Asn272Ser
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.692A>G
  hgvsp: ENSP00000280699.9:p.Ile232Val
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.941A>G
  hgvsp: ENSP00000280700.5:p.Asn314Ser
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.941A>G
  hgvsp: ENSP00000387430.1:p.Asn314Ser
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.932A>G
  hgvsp: ENSP00000307980.5:p.Asn311Ser
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.487A>G
  hgvsp: ENSP00000395878.2:p.Ile163Val
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 305
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 614
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 77
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 418
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 123
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 107
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 196
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 513
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 42301
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 162
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 262
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11754
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 289
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 250
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2931
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 160
  bin: 6.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 62
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 69
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 109
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2031
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 51716
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 70
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 66
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 337
  bin: 8.25e1
  variant carriers: 0
hgvs: p.Asn314Ser
num of homozygotes: 0
population: East Asian
population: African
population: South Asian
population: Latino
population: European (Non-Finnish)
population: Other
population: European (Finnish)
reference allele: T
site quality: QD
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: FS
site quality: MQRankSum
site quality: MQ
site quality: VQSLOD
site quality: DP
site quality: ClippingRankSum
site quality: BaseQRankSum

http://identifiers.org/exac.variant/3-25778897-C-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25778897
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25778897
    reference: chr 3
allele count: 1
allele frequency: 8.306889734345666e-6
allele num: 120382
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: stop_gained
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.931G>T
  hgvsp: ENSP00000387430.1:p.Glu311Ter
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.955G>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.477G>T
  hgvsp: ENST00000422724.2:c.477G>T(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: stop_gained
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.922G>T
  hgvsp: ENSP00000307980.5:p.Glu308Ter
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: stop_gained
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.931G>T
  hgvsp: ENSP00000379886.3:p.Glu311Ter
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: stop_gained
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.805G>T
  hgvsp: ENSP00000389888.2:p.Glu269Ter
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.682G>T
  hgvsp: ENST00000280699.9:c.682G>T(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: stop_gained
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.931G>T
  hgvsp: ENSP00000280700.5:p.Glu311Ter
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: stop gained
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 497
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 62
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 421
  bin: 4.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 289
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2964
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 69
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 107
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 78
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 160
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 305
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12025
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 41943
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 154
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 198
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 123
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 619
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 315
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 109
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 262
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 84
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 41
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 335
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2035
  bin: 9.75e1
  variant carriers: 1
hgvs: p.Glu311Ter
num of homozygotes: 0
population: Other
population: East Asian
population: African
population: European (Non-Finnish)
population: South Asian
population: Latino
population: European (Finnish)
reference allele: C
site quality: ReadPosRankSum
site quality: MQ
site quality: VQSLOD
site quality: DP
site quality: MQRankSum
site quality: FS
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: QD
site quality: BaseQRankSum

3-25778897-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25778897
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25778897
    reference: chr 3
allele count: 6
allele frequency: 4.9841338406074e-5
allele num: 120382
alternate allele: T
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.931G>A
  hgvsp: ENSP00000280700.5:p.Glu311Lys
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.955G>A
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.931G>A
  hgvsp: ENSP00000379886.3:p.Glu311Lys
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.805G>A
  hgvsp: ENSP00000389888.2:p.Glu269Lys
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.477G>A
  hgvsp: ENST00000422724.2:c.477G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.922G>A
  hgvsp: ENSP00000307980.5:p.Glu308Lys
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.931G>A
  hgvsp: ENSP00000387430.1:p.Glu311Lys
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.682G>A
  hgvsp: ENST00000280699.9:c.682G>A(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 421
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 154
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 198
  bin: 5.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 315
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2964
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 62
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 123
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 109
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 305
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 497
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 41943
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 262
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 619
  bin: 3.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 78
  bin: 8.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 12025
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 160
  bin: 6.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 69
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 289
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 107
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 86
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 84
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3818
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 600
  bin: 7.75e1
  variant carriers: 0
hgvs: p.Glu311Lys
num of homozygotes: 0
population: South Asian
population: Latino
population: African
population: European (Finnish)
population: Other
population: East Asian
population: European (Non-Finnish)
reference allele: C
site quality: MQ
site quality: QD
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: DP
site quality: BaseQRankSum
site quality: FS
site quality: VQSLOD
site quality: ClippingRankSum

3-25778898-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25778898
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25778898
    reference: chr 3
allele count: 1
allele frequency: 8.30813199960121e-6
allele num: 120364
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.921C>T
  hgvsp: ENST00000308710.5:c.921C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.930C>T
  hgvsp: ENST00000396649.3:c.930C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.954C>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.681C>T
  hgvsp: ENSP00000280699.9:p.Ala228Val
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.930C>T
  hgvsp: ENST00000428257.1:c.930C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.476C>T
  hgvsp: ENSP00000395878.2:p.Ala159Val
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.804C>T
  hgvsp: ENST00000417874.2:c.804C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.930C>T
  hgvsp: ENST00000280700.5:c.930C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
canonical: false
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 123
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 152
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 159
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 427
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2973
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 262
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 196
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 497
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 41887
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 107
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 289
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 77
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 109
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 322
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 627
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 62
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 308
  bin: 4.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 12053
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 69
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 703
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 87
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 51574
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 597
  bin: 7.75e1
  variant carriers: 0
hgvs: p.Ala228Val
num of homozygotes: 0
population: Latino
population: African
population: Other
population: European (Finnish)
population: European (Non-Finnish)
population: East Asian
population: South Asian
reference allele: G
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: MQ
site quality: ClippingRankSum
site quality: DP
site quality: BaseQRankSum
site quality: MQRankSum
site quality: FS
site quality: QD
site quality: VQSLOD

http://identifiers.org/exac.variant/3-25778902-C-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25778902
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25778902
    reference: chr 3
allele count: 1
allele frequency: 8.30937463646486e-6
allele num: 120346
alternate allele: A
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.926G>T
  hgvsp: ENSP00000280700.5:p.Cys309Phe
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.917G>T
  hgvsp: ENSP00000307980.5:p.Cys306Phe
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.926G>T
  hgvsp: ENSP00000379886.3:p.Cys309Phe
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.677G>T
  hgvsp: ENSP00000280699.9:p.Val227Leu
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.800G>T
  hgvsp: ENSP00000389888.2:p.Cys267Phe
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.926G>T
  hgvsp: ENSP00000387430.1:p.Cys309Phe
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.472G>T
  hgvsp: ENSP00000395878.2:p.Val158Leu
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.950G>T
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 77
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 305
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 289
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 69
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 109
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 148
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 518
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 380
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 124
  bin: 6.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 419
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 196
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2958
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 107
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 617
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 41780
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12118
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 159
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 262
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 62
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 168
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 664
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 57
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 80
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3797
  bin: 6.75e1
  variant carriers: 0
hgvs: p.Cys309Phe
num of homozygotes: 0
population: European (Non-Finnish)
population: African
population: Latino
population: East Asian
population: Other
population: European (Finnish)
population: South Asian
reference allele: C
site quality: ReadPosRankSum
site quality: MQ
site quality: FS
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: DP
site quality: QD
site quality: MQRankSum
site quality: ClippingRankSum
site quality: VQSLOD

3-25778903-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25778903
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25778903
    reference: chr 3
allele count: 1
allele frequency: 8.309788931361144e-6
allele num: 120340
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.471T>C
  hgvsp: ENST00000422724.2:c.471T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.799T>C
  hgvsp: ENSP00000389888.2:p.Cys267Arg
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.676T>C
  hgvsp: ENST00000280699.9:c.676T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.916T>C
  hgvsp: ENSP00000307980.5:p.Cys306Arg
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.925T>C
  hgvsp: ENSP00000379886.3:p.Cys309Arg
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.925T>C
  hgvsp: ENSP00000280700.5:p.Cys309Arg
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.949T>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.925T>C
  hgvsp: ENSP00000387430.1:p.Cys309Arg
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 421
  bin: 4.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 123
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 145
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 289
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 262
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 107
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 196
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 41785
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 384
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 109
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 513
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2957
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 618
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12116
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 62
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 77
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 69
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 305
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 159
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 48
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2029
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 168
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 330
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 33
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 778
  bin: 2.25e1
  variant carriers: 0
hgvs: p.Cys309Arg
num of homozygotes: 0
population: European (Non-Finnish)
population: Other
population: European (Finnish)
population: East Asian
population: South Asian
population: Latino
population: African
reference allele: A
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: VQSLOD
site quality: DP
site quality: QD
site quality: MQRankSum
site quality: FS
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: MQ

3-25778905-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25778905
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25778905
    reference: chr 3
allele count: 1
allele frequency: 8.311861025683651e-6
allele num: 120310
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.923G>A
  hgvsp: ENSP00000387430.1:p.Arg308Gln
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.469G>A
  hgvsp: ENSP00000395878.2:p.Gly157Ser
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.947G>A
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.797G>A
  hgvsp: ENSP00000389888.2:p.Arg266Gln
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.923G>A
  hgvsp: ENSP00000280700.5:p.Arg308Gln
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.674G>A
  hgvsp: ENSP00000280699.9:p.Gly226Ser
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.914G>A
  hgvsp: ENSP00000307980.5:p.Arg305Gln
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.923G>A
  hgvsp: ENSP00000379886.3:p.Arg308Gln
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 289
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 622
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 77
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 263
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 423
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2975
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 123
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 413
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 141
  bin: 1.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 307
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 528
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 41699
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12135
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 159
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 69
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 62
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 107
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 109
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 196
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3793
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 582
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 661
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 821
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 43
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 1.25e1
  variant carriers: 0
hgvs: p.Arg308Gln
num of homozygotes: 0
population: European (Finnish)
population: East Asian
population: Other
population: South Asian
population: Latino
population: African
population: European (Non-Finnish)
reference allele: C
site quality: ClippingRankSum
site quality: DP
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: VQSLOD
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: MQ
site quality: FS
site quality: QD

3-25778906-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25778906
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25778906
    reference: chr 3
allele count: 1
allele frequency: 8.314487162431821e-6
allele num: 120272
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.796C>T
  hgvsp: ENSP00000389888.2:p.Arg266Trp
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.922C>T
  hgvsp: ENSP00000387430.1:p.Arg308Trp
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.913C>T
  hgvsp: ENSP00000307980.5:p.Arg305Trp
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.673C>T
  hgvsp: ENST00000280699.9:c.673C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.946C>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.922C>T
  hgvsp: ENSP00000379886.3:p.Arg308Trp
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.922C>T
  hgvsp: ENSP00000280700.5:p.Arg308Trp
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.468C>T
  hgvsp: ENST00000422724.2:c.468C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: missense
filter: VQSRTrancheSNP99.60to99.80
genotype depth: GenotypeDepth
  all individuals: 41611
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 123
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2978
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 263
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 540
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 69
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 141
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 436
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 289
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 424
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 107
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 196
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 159
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 77
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 62
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 634
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 307
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12171
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 109
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 92
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 87
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 860
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 654
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 170
  bin: 8.75e1
  variant carriers: 0
hgvs: p.Arg308Trp
num of homozygotes: 0
population: African
population: South Asian
population: Latino
population: European (Non-Finnish)
population: European (Finnish)
population: East Asian
population: Other
reference allele: G
site quality: QD
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: DP
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: MQRankSum
site quality: ClippingRankSum
site quality: FS
site quality: MQ

3-25778913-T-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25778913
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25778913
    reference: chr 3
allele count: 1
allele frequency: 8.335278231587371e-6
allele num: 119972
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.915A>G
  hgvsp: ENST00000428257.1:c.915A>G(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.915A>G
  hgvsp: ENST00000280700.5:c.915A>G(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.666A>G
  hgvsp: ENSP00000280699.9:p.Asp223Gly
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.906A>G
  hgvsp: ENST00000308710.5:c.906A>G(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.461A>G
  hgvsp: ENSP00000395878.2:p.Asp154Gly
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.789A>G
  hgvsp: ENST00000417874.2:c.789A>G(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.939A>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.915A>G
  hgvsp: ENST00000396649.3:c.915A>G(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
canonical: false
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 123
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2967
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 305
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 159
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 289
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 107
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 202
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 614
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 41116
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 708
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12212
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 696
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 69
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 77
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 263
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 109
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 421
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 62
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 197
  bin: 5.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 648
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 73
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 573
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1228
  bin: 2.25e1
  variant carriers: 0
hgvs: p.Asp223Gly
num of homozygotes: 0
population: Other
population: European (Non-Finnish)
population: European (Finnish)
population: African
population: East Asian
population: Latino
population: South Asian
reference allele: T
site quality: DP
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: QD
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: FS
site quality: MQRankSum
site quality: MQ
site quality: ReadPosRankSum

3-25778927-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25778927
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25778927
    reference: chr 3
allele count: 1
allele frequency: 8.473427331887202e-6
allele num: 118016
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.447C>T
  hgvsp: ENST00000422724.2:c.447C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.901C>T
  hgvsp: ENSP00000280700.5:p.Leu301Phe
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.901C>T
  hgvsp: ENSP00000379886.3:p.Leu301Phe
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.652C>T
  hgvsp: ENST00000280699.9:c.652C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.892C>T
  hgvsp: ENSP00000307980.5:p.Leu298Phe
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.925C>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.775C>T
  hgvsp: ENSP00000389888.2:p.Leu259Phe
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.901C>T
  hgvsp: ENSP00000387430.1:p.Leu301Phe
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 528
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 305
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 38699
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 107
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2929
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1628
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11852
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 262
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 62
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 109
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 289
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 123
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 423
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 77
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2233
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 196
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 621
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 159
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 69
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 45
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2029
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 524
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 305
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 377
  bin: 3.25e1
  variant carriers: 0
hgvs: p.Leu301Phe
num of homozygotes: 0
population: South Asian
population: East Asian
population: European (Finnish)
population: African
population: Latino
population: European (Non-Finnish)
population: Other
reference allele: G
site quality: QD
site quality: BaseQRankSum
site quality: MQRankSum
site quality: FS
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: DP
site quality: ReadPosRankSum
site quality: MQ
site quality: ClippingRankSum

http://identifiers.org/exac.variant/3-25778931-C-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25778931
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25778931
    reference: chr 3
allele count: 2
allele frequency: 1.698686915014694e-5
allele num: 117738
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.897G>T
  hgvsp: ENSP00000387430.1:p.Glu299Asp
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.921G>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.888G>T
  hgvsp: ENSP00000307980.5:p.Glu296Asp
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.897G>T
  hgvsp: ENSP00000280700.5:p.Glu299Asp
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.897G>T
  hgvsp: ENSP00000379886.3:p.Glu299Asp
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.771G>T
  hgvsp: ENSP00000389888.2:p.Glu257Asp
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.443G>T
  hgvsp: ENSP00000395878.2:p.Arg148Ile
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.648G>T
  hgvsp: ENSP00000280699.9:p.Arg217Ile
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1772
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 617
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 262
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 37
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 158
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 123
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2457
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 197
  bin: 5.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 290
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 564
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 77
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 69
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 421
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 62
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11813
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2943
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 305
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 38323
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 109
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 107
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 160
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 499
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 133
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 16
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 406
  bin: 3.25e1
  variant carriers: 0
hgvs: p.Glu299Asp
num of homozygotes: 0
population: European (Finnish)
population: Other
population: Latino
population: African
population: East Asian
population: South Asian
population: European (Non-Finnish)
reference allele: C
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: FS
site quality: DP
site quality: MQ
site quality: VQSLOD
site quality: MQRankSum
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: QD

3-25778936-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25778936
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25778936
    reference: chr 3
allele count: 1
allele frequency: 8.652764558276369e-6
allele num: 115570
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.892C>T
  hgvsp: ENSP00000379886.3:p.Pro298Ser
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.438C>T
  hgvsp: ENST00000422724.2:c.438C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.883C>T
  hgvsp: ENSP00000307980.5:p.Pro295Ser
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.892C>T
  hgvsp: ENSP00000387430.1:p.Pro298Ser
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.643C>T
  hgvsp: ENST00000280699.9:c.643C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.916C>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.766C>T
  hgvsp: ENSP00000389888.2:p.Pro256Ser
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.892C>T
  hgvsp: ENSP00000280700.5:p.Pro298Ser
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 617
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 308
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 59
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 263
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 77
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 62
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 421
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3901
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 158
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2815
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 35764
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 123
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11405
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1045
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 69
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 109
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 289
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2918
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 196
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 107
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 22
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 16
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 25
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 308
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 289
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 217
  bin: 5.75e1
  variant carriers: 0
hgvs: p.Pro298Ser
num of homozygotes: 0
population: European (Non-Finnish)
population: European (Finnish)
population: Other
population: African
population: Latino
population: East Asian
population: South Asian
reference allele: G
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: ClippingRankSum
site quality: VQSLOD
site quality: BaseQRankSum
site quality: QD
site quality: InbreedingCoeff
site quality: FS
site quality: DP
site quality: MQ

3-25778939-T-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25778939
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25778939
    reference: chr 3
allele count: 1
allele frequency: 8.798324798958279e-6
allele num: 113658
alternate allele: A
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.889A>T
  hgvsp: ENSP00000280700.5:p.Asn297Tyr
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.913A>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.889A>T
  hgvsp: ENSP00000379886.3:p.Asn297Tyr
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.640A>T
  hgvsp: ENST00000280699.9:c.640A>T(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.880A>T
  hgvsp: ENSP00000307980.5:p.Asn294Tyr
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.889A>T
  hgvsp: ENSP00000387430.1:p.Asn297Tyr
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.763A>T
  hgvsp: ENSP00000389888.2:p.Asn255Tyr
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.435A>T
  hgvsp: ENST00000422724.2:c.435A>T(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: missense
filter: VQSRTrancheSNP99.60to99.80
genotype depth: GenotypeDepth
  all individuals: 10877
  bin: 2.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 107
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2857
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 408
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 109
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 158
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 195
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 300
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3748
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33647
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 123
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 62
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 69
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 81
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 262
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 289
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 77
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5288
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 605
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1442
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 96
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7672
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 158
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1208
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1092
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 186
  bin: 5.75e1
  variant carriers: 0
hgvs: p.Asn297Tyr
num of homozygotes: 0
population: Latino
population: Other
population: European (Finnish)
population: East Asian
population: African
population: European (Non-Finnish)
population: South Asian
reference allele: T
site quality: BaseQRankSum
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: QD
site quality: ClippingRankSum
site quality: DP
site quality: FS
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: MQ

3-25778943-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25778943
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25778943
    reference: chr 3
allele count: 4
allele frequency: 3.641527985142566e-5
allele num: 109844
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.759T>C
  hgvsp: ENST00000417874.2:c.759T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.909T>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.885T>C
  hgvsp: ENST00000280700.5:c.885T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.885T>C
  hgvsp: ENST00000428257.1:c.885T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.431T>C
  hgvsp: ENSP00000395878.2:p.Ile144Thr
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.876T>C
  hgvsp: ENST00000308710.5:c.876T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.636T>C
  hgvsp: ENSP00000280699.9:p.Ile213Thr
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.885T>C
  hgvsp: ENST00000396649.3:c.885T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
canonical: false
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 194
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 298
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 289
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 107
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2227
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29305
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8120
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 62
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2741
  bin: 3.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 5559
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 616
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 157
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 77
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 260
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 109
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 123
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 397
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 158
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 69
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9832
  bin: 2.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 55
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 220
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 37465
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 19
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 236
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1747
  bin: 3.25e1
  variant carriers: 0
hgvs: p.Ile213Thr
num of homozygotes: 0
population: Other
population: Latino
population: European (Finnish)
population: East Asian
population: European (Non-Finnish)
population: South Asian
population: African
reference allele: A
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: MQ
site quality: QD
site quality: BaseQRankSum
site quality: FS
site quality: DP
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: MQRankSum

3-25778944-T-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25778944
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25778944
    reference: chr 3
allele count: 1
allele frequency: 9.288155743795512e-6
allele num: 107664
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: splice_region_variant
  consequence: NMD_transcript_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.635A>C
  hgvsp: ENSP00000280699.9:p.Ile213Leu
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: splice_region_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.758A>C
  hgvsp: ENSP00000389888.2:p.Tyr253Ser
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: splice_region_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.884A>C
  hgvsp: ENSP00000387430.1:p.Tyr295Ser
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: splice_region_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.875A>C
  hgvsp: ENSP00000307980.5:p.Tyr292Ser
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: splice_region_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.430A>C
  hgvsp: ENSP00000395878.2:p.Ile144Leu
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  consequence: splice_region_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.884A>C
  hgvsp: ENSP00000379886.3:p.Tyr295Ser
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  consequence: splice_region_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.908A>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: missense_variant
  consequence: splice_region_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.884A>C
  hgvsp: ENSP00000280700.5:p.Tyr295Ser
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 194
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 26960
  bin: 2.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 77
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 392
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 69
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10001
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 208
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2520
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6553
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2660
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9078
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 109
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 62
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 158
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 123
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 295
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 289
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 257
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 588
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 107
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2310
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 253
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2213
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 557
  bin: 5.25e1
  variant carriers: 0
hgvs: p.Tyr295Ser
num of homozygotes: 0
population: African
population: South Asian
population: Latino
population: European (Non-Finnish)
population: European (Finnish)
population: Other
population: East Asian
reference allele: T
site quality: InbreedingCoeff
site quality: QD
site quality: BaseQRankSum
site quality: VQSLOD
site quality: ClippingRankSum
site quality: FS
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: DP
site quality: MQ

3-25778958-AG-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25778958
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25778957
    reference: chr 3
allele count: 1
allele frequency: 1.038529442309689e-5
allele num: 96290
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.906-13delC
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-13delC
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-13delC
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.882-13delC
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.873-13delC
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.882-13delC
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.756-13delC
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.882-13delC
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 470
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 289
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4076
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 953
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15011
  bin: 2.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 18959
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11281
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6427
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 62
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 292
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 109
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 158
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1399
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 123
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 107
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 254
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 194
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 69
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 368
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 77
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 22319
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4423
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 347
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 301
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2119
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 525
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 513
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4575
  bin: 3.25e1
  variant carriers: 0
num of homozygotes: 0
population: East Asian
population: European (Finnish)
population: South Asian
population: Other
population: Latino
population: European (Non-Finnish)
population: African
reference allele: AG
site quality: VQSLOD
site quality: MQ
site quality: FS
site quality: MQRankSum
site quality: ClippingRankSum
site quality: ReadPosRankSum
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: DP
site quality: QD

3-25778959-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25778959
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25778959
    reference: chr 3
allele count: 2
allele frequency: 2.154568763062073e-5
allele num: 92826
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-13C>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.882-13C>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.756-13C>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.906-13C>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.873-13C>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.882-13C>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.882-13C>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-13C>T
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 382
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 296
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6026
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 506
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 19853
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 107
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11582
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13776
  bin: 2.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 291
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 108
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1048
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 60
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 125
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 158
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4282
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 251
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1479
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 195
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 70
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 80
  bin: 8.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 577
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 597
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 313
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 596
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 355
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4672
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 598
  bin: 4.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 596
  bin: 5.25e1
  variant carriers: 0
num of homozygotes: 0
population: South Asian
population: European (Finnish)
population: Other
population: European (Non-Finnish)
population: Latino
population: African
population: East Asian
reference allele: G
site quality: MQRankSum
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: QD
site quality: FS
site quality: MQ
site quality: ClippingRankSum
site quality: ReadPosRankSum
site quality: DP

3-25778959-G-GA
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25778959
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25778960
    reference: chr 3
allele count: 35
allele frequency: 3.770495335358628e-4
allele num: 92826
alternate allele: GA
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.906-14dupT
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.882-14dupT
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-14dupT
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.756-14dupT
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.882-14dupT
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.882-14dupT
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-14dupT
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.873-14dupT
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 70
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 296
  bin: 4.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1479
  bin: 3.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 4282
  bin: 1.75e1
  variant carriers: 8
genotype depth: GenotypeDepth
  all individuals: 19853
  bin: 1.25e1
  variant carriers: 9
genotype depth: GenotypeDepth
  all individuals: 195
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 382
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 125
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 506
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 158
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1048
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6026
  bin: 2.75e1
  variant carriers: 5
genotype depth: GenotypeDepth
  all individuals: 11582
  bin: 7.5e0
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 13776
  bin: 2.25e1
  variant carriers: 10
genotype depth: GenotypeDepth
  all individuals: 60
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 291
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 108
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 80
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 251
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 107
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 598
  bin: 4.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 596
  bin: 2.5e0
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 265
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 153
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2034
  bin: 9.75e1
  variant carriers: 24
genotype quality: GenotypeQuality
  all individuals: 628
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 22653
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1186
  bin: 6.75e1
  variant carriers: 0
num of homozygotes: 0
population: Latino
population: African
population: East Asian
population: European (Non-Finnish)
population: Other
population: European (Finnish)
population: South Asian
reference allele: G
site quality: QD
site quality: InbreedingCoeff
site quality: DP
site quality: FS
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: MQ
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: MQRankSum

3-25778959-GA-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25778959
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25778958
    reference: chr 3
allele count: 2
allele frequency: 2.154568763062073e-5
allele num: 92826
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-14delT
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.906-14delT
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-14delT
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.873-14delT
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.882-14delT
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.756-14delT
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.882-14delT
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.882-14delT
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 296
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 506
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4282
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1048
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 125
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11582
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 108
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 251
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1479
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13776
  bin: 2.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 6026
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 19853
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 60
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 382
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 195
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 80
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 70
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 158
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 107
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 291
  bin: 9.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2083
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 577
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1432
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1186
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 598
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4672
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 217
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 313
  bin: 7.25e1
  variant carriers: 0
num of homozygotes: 0
population: African
population: South Asian
population: East Asian
population: European (Non-Finnish)
population: European (Finnish)
population: Latino
population: Other
reference allele: GA
site quality: ReadPosRankSum
site quality: FS
site quality: DP
site quality: VQSLOD
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: MQ
site quality: QD
site quality: BaseQRankSum

3-25778964-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25778964
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25778964
    reference: chr 3
allele count: 4
allele frequency: 4.392611627242977e-5
allele num: 91062
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-18T>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-18T>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.873-18T>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.906-18T>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.882-18T>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.882-18T>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.882-18T>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.756-18T>C
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 76
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 288
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10131
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 123
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 989
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 162
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 60
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 23361
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 13193
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 192
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1666
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 249
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4448
  bin: 1.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 448
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 107
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 69
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4334
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 365
  bin: 4.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 108
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 289
  bin: 9.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1028
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 438
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 24971
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5511
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 353
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 447
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 276
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 568
  bin: 1.75e1
  variant carriers: 0
num of homozygotes: 0
population: African
population: Latino
population: European (Non-Finnish)
population: Other
population: European (Finnish)
population: South Asian
population: East Asian
reference allele: A
site quality: FS
site quality: QD
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: DP
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: MQ
site quality: InbreedingCoeff
site quality: VQSLOD

http://identifiers.org/exac.variant/3-25778967-A-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25778967
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25778967
    reference: chr 3
allele count: 1
allele frequency: 1.123545009213069e-5
allele num: 89004
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.906-21T>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.882-21T>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-21T>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.873-21T>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.882-21T>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.882-21T>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.756-21T>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-21T>G
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 8462
  bin: 2.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 107
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2022
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 69
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 364
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 906
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13602
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3697
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 452
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 192
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 108
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 288
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 249
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4943
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 24468
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 60
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 76
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 162
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 123
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 289
  bin: 9.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2187
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 24967
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 306
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6581
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 216
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 610
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 267
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 684
  bin: 4.25e1
  variant carriers: 0
num of homozygotes: 0
population: East Asian
population: African
population: European (Non-Finnish)
population: Latino
population: Other
population: South Asian
population: European (Finnish)
reference allele: A
site quality: MQ
site quality: MQRankSum
site quality: VQSLOD
site quality: FS
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: ReadPosRankSum
site quality: DP
site quality: BaseQRankSum
site quality: QD

http://identifiers.org/exac.variant/3-25778980-A-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25778980
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25778980
    reference: chr 3
allele count: 1
allele frequency: 1.249250449730162e-5
allele num: 80048
alternate allele: C
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.882-34T>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.882-34T>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.882-34T>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.906-34T>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-34T>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.873-34T>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-34T>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.756-34T>G
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 162
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 69
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4364
  bin: 2.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1784
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 24309
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 420
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 192
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3905
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6759
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 360
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 250
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16272
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 60
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 123
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 106
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 642
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 76
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 108
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 287
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 289
  bin: 9.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7756
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 336
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 267
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 23103
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 217
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 867
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 281
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2018
  bin: 9.75e1
  variant carriers: 1
num of homozygotes: 0
population: European (Finnish)
population: Latino
population: East Asian
population: European (Non-Finnish)
population: Other
population: African
population: South Asian
reference allele: A
site quality: ClippingRankSum
site quality: MQ
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: QD
site quality: VQSLOD
site quality: FS
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: DP

3-25778993-T-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25778993
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25778993
    reference: chr 3
allele count: 1
allele frequency: 1.425801300330786e-5
allele num: 70136
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.756-47A>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.873-47A>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.882-47A>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-47A>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.906-47A>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.882-47A>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.882-47A>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-47A>C
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: intron
filter: VQSRTrancheSNP99.60to99.80
genotype depth: GenotypeDepth
  all individuals: 3107
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 106
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 69
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 60
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 419
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 76
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 359
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 600
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 250
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8005
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20471
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 108
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 286
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 289
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20337
  bin: 1.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 4395
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 123
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 162
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 192
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1031
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6076
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 263
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7746
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3528
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 215
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 260
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2010
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 747
  bin: 2.5e0
  variant carriers: 0
num of homozygotes: 0
population: South Asian
population: Latino
population: European (Finnish)
population: European (Non-Finnish)
population: East Asian
population: Other
population: African
reference allele: T
site quality: VQSLOD
site quality: ReadPosRankSum
site quality: FS
site quality: MQRankSum
site quality: QD
site quality: DP
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: MQ
site quality: InbreedingCoeff

http://identifiers.org/exac.variant/3-25781027-CA-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781027
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781026
    reference: chr 3
allele count: 1
allele frequency: 8.406186953597848e-6
allele num: 118960
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.881+40delT
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2082delT
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.905+40delT
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.755+40delT
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.872+40delT
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.881+40delT
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.881+40delT
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2082delT
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 95
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 19
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 374
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 199
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 389
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1392
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2192
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1598
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 27652
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 960
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 114
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 592
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15008
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 77
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9879
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 61
  bin: 6.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 851
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 116
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 326
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 582
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 492
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1031
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 977
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 78
  bin: 1.75e1
  variant carriers: 0
num of homozygotes: 0
population: South Asian
population: European (Non-Finnish)
population: Other
population: European (Finnish)
population: East Asian
population: African
population: Latino
reference allele: CA
site quality: FS
site quality: ReadPosRankSum
site quality: InbreedingCoeff
site quality: MQ
site quality: ClippingRankSum
site quality: VQSLOD
site quality: BaseQRankSum
site quality: QD
site quality: MQRankSum
site quality: DP

3-25781039-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781039
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781039
    reference: chr 3
allele count: 2
allele frequency: 1.672073036150219e-5
allele num: 119612
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.872+29T>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.755+29T>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2093T>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2093T>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.905+29T>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.881+29T>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.881+29T>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.881+29T>C
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 25
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 789
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1584
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 464
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1165
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9919
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 28263
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 77
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 44
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 201
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 589
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 115
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16571
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 367
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 390
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 61
  bin: 6.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 47
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 552
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7999
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 357
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 43161
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1590
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 21
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 102
  bin: 5.25e1
  variant carriers: 0
num of homozygotes: 0
population: South Asian
population: African
population: Other
population: European (Non-Finnish)
population: Latino
population: European (Finnish)
population: East Asian
reference allele: A
site quality: ReadPosRankSum
site quality: BaseQRankSum
site quality: DP
site quality: FS
site quality: MQRankSum
site quality: ClippingRankSum
site quality: MQ
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: QD

3-25781051-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781051
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781051
    reference: chr 3
allele count: 1
allele frequency: 8.309098462816784e-6
allele num: 120350
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.755+17G>A
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.881+17G>A
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2105G>A
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.905+17G>A
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.881+17G>A
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.872+17G>A
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.881+17G>A
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2105G>A
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 61
  bin: 6.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 364
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1593
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 486
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 165
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17378
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 446
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 110
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 28724
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 76
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9997
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 390
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 584
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 198
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1601
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1646
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 329
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 173
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 550
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 160
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 205
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 18
  bin: 7.5e0
  variant carriers: 0
num of homozygotes: 0
population: European (Finnish)
population: Latino
population: African
population: East Asian
population: South Asian
population: Other
population: European (Non-Finnish)
reference allele: C
site quality: FS
site quality: MQRankSum
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: ReadPosRankSum
site quality: MQ
site quality: VQSLOD
site quality: DP
site quality: InbreedingCoeff
site quality: QD

3-25781056-C-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781056
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781056
    reference: chr 3
allele count: 1
allele frequency: 8.285141427364165e-6
allele num: 120698
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.881+12G>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.881+12G>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.755+12G>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.872+12G>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2110G>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.905+12G>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2110G>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.881+12G>C
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 582
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10041
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 197
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 391
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 102
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17493
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1595
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 288
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20
  bin: 8.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 110
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 364
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 321
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 76
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 60
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 28954
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 331
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 50
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 143
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 111
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 99
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 13
  bin: 2.5e0
  variant carriers: 0
num of homozygotes: 0
population: European (Non-Finnish)
population: European (Finnish)
population: African
population: East Asian
population: Latino
population: Other
population: South Asian
reference allele: C
site quality: QD
site quality: MQ
site quality: VQSLOD
site quality: MQRankSum
site quality: DP
site quality: FS
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: ReadPosRankSum

3-25781058-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781058
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781058
    reference: chr 3
allele count: 3
allele frequency: 2.482375136530632e-5
allele num: 120852
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.872+10C>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.755+10C>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.881+10C>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2112C>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.881+10C>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.905+10C>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2112C>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.881+10C>T
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: intron
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 29048
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 196
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 80
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1598
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 248
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 364
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10023
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 109
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 582
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17600
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 394
  bin: 9.75e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 197
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 60
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 19
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 77
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 275
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8208
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 86
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 61
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 51
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1636
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10
  bin: 7.5e0
  variant carriers: 0
num of homozygotes: 0
population: East Asian
population: African
population: European (Finnish)
population: Latino
population: South Asian
population: Other
population: European (Non-Finnish)
reference allele: G
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: MQ
site quality: FS
site quality: InbreedingCoeff
site quality: DP
site quality: VQSLOD
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: QD

3-25781060-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781060
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781060
    reference: chr 3
allele count: 30
allele frequency: 2.480609899287238e-4
allele num: 120938
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.881+8C>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.872+8C>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.755+8C>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.881+8C>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2114C>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.881+8C>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: splice_region_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.905+8C>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2114C>T
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: splice region
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 29087
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33
  bin: 7.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 83
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 60
  bin: 6.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 76
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 580
  bin: 4.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 10013
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 198
  bin: 5.25e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 19
  bin: 8.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 44
  bin: 7.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 214
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 182
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17608
  bin: 2.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 111
  bin: 5.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 364
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 407
  bin: 9.75e1
  variant carriers: 18
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1591
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 53
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 76
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1633
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 1.75e1
  variant carriers: 0
hgvs: c.881+8C>T
num of homozygotes: 0
population: South Asian
population: African
population: European (Non-Finnish)
population: European (Finnish)
population: Latino
population: East Asian
population: Other
reference allele: G
site quality: InbreedingCoeff
site quality: FS
site quality: DP
site quality: QD
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: MQRankSum
site quality: VQSLOD
site quality: ReadPosRankSum
site quality: MQ

3-25781070-T-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781070
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781070
    reference: chr 3
allele count: 1
allele frequency: 8.254094030639197e-6
allele num: 121152
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: splice_region_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.879A>G
  hgvsp: ENST00000396649.3:c.879A>G(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  consequence: splice_region_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.903A>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2124A>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: splice_region_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.870A>G
  hgvsp: ENST00000308710.5:c.870A>G(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: splice_region_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.879A>G
  hgvsp: ENST00000428257.1:c.879A>G(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  consequence: splice_region_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.753A>G
  hgvsp: ENST00000417874.2:c.753A>G(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  consequence: splice_region_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.879A>G
  hgvsp: ENST00000280700.5:c.879A>G(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2124A>G
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: splice region
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 195
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 578
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1588
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17618
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 109
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29294
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 365
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 116
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10063
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 89
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 39
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 76
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 389
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 59
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 26
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1870
  bin: 9.75e1
  variant carriers: 1
hgvs: c.879A>G
num of homozygotes: 0
population: European (Finnish)
population: African
population: European (Non-Finnish)
population: South Asian
population: Latino
population: East Asian
population: Other
reference allele: T
site quality: MQ
site quality: ReadPosRankSum
site quality: DP
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: FS
site quality: MQRankSum
site quality: BaseQRankSum
site quality: VQSLOD
site quality: QD

3-25781072-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781072
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781072
    reference: chr 3
allele count: 1
allele frequency: 8.25218682950982e-6
allele num: 121180
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2126C>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.751C>T
  hgvsp: ENSP00000389888.2:p.Pro251Ser
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.868C>T
  hgvsp: ENSP00000307980.5:p.Pro290Ser
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.877C>T
  hgvsp: ENSP00000280700.5:p.Pro293Ser
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.877C>T
  hgvsp: ENSP00000387430.1:p.Pro293Ser
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.877C>T
  hgvsp: ENSP00000379886.3:p.Pro293Ser
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.901C>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2126C>T
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 109
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29316
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 577
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 38
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 365
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 103
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10065
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17615
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1592
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 195
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 76
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 79
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 389
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 59
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 34
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 45410
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 117
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 848
  bin: 8.25e1
  variant carriers: 0
hgvs: p.Pro293Ser
num of homozygotes: 0
population: European (Non-Finnish)
population: European (Finnish)
population: Other
population: African
population: South Asian
population: Latino
population: East Asian
reference allele: G
site quality: BaseQRankSum
site quality: MQ
site quality: VQSLOD
site quality: ReadPosRankSum
site quality: InbreedingCoeff
site quality: DP
site quality: FS
site quality: QD
site quality: ClippingRankSum
site quality: MQRankSum

3-25781075-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781075
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781075
    reference: chr 3
allele count: 1
allele frequency: 8.247694769311978e-6
allele num: 121246
alternate allele: G
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.874T>C
  hgvsp: ENSP00000280700.5:p.Phe292Leu
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.898T>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.748T>C
  hgvsp: ENSP00000389888.2:p.Phe250Leu
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.865T>C
  hgvsp: ENSP00000307980.5:p.Phe289Leu
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.874T>C
  hgvsp: ENSP00000379886.3:p.Phe292Leu
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2129T>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2129T>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.874T>C
  hgvsp: ENSP00000387430.1:p.Phe292Leu
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 110
  bin: 5.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 72
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 34
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17622
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 76
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1591
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 59
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 578
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 194
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 59
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29357
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 365
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10074
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 388
  bin: 9.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 32
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1664
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 849
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 330
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1869
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 45465
  bin: 6.25e1
  variant carriers: 0
hgvs: p.Phe292Leu
num of homozygotes: 0
population: East Asian
population: European (Non-Finnish)
population: African
population: Latino
population: European (Finnish)
population: South Asian
population: Other
reference allele: A
site quality: FS
site quality: MQ
site quality: MQRankSum
site quality: QD
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: VQSLOD
site quality: DP
site quality: BaseQRankSum
site quality: ReadPosRankSum

3-25781077-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781077
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781077
    reference: chr 3
allele count: 2
allele frequency: 1.649321304283287e-5
allele num: 121262
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.863G>A
  hgvsp: ENSP00000307980.5:p.Arg288Gln
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.872G>A
  hgvsp: ENSP00000379886.3:p.Arg291Gln
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.896G>A
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.872G>A
  hgvsp: ENSP00000280700.5:p.Arg291Gln
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2131G>A
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.872G>A
  hgvsp: ENSP00000387430.1:p.Arg291Gln
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2131G>A
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.746G>A
  hgvsp: ENSP00000389888.2:p.Arg249Gln
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 3
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1598
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 52
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 59
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17598
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10082
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 367
  bin: 4.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 64
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 109
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 194
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 580
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29379
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 389
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 76
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 329
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 848
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 32
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 17
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1617
  bin: 7.75e1
  variant carriers: 0
hgvs: p.Arg291Gln
num of homozygotes: 0
population: Latino
population: Other
population: East Asian
population: African
population: South Asian
population: European (Finnish)
population: European (Non-Finnish)
reference allele: C
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: DP
site quality: MQRankSum
site quality: BaseQRankSum
site quality: QD
site quality: ReadPosRankSum
site quality: FS
site quality: VQSLOD
site quality: MQ

3-25781078-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781078
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781078
    reference: chr 3
allele count: 1
allele frequency: 8.244294947896055e-6
allele num: 121296
alternate allele: A
annotation: Annotation
  canonical: true
  consequence: stop_gained
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.871C>T
  hgvsp: ENSP00000280700.5:p.Arg291Ter
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: stop_gained
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.862C>T
  hgvsp: ENSP00000307980.5:p.Arg288Ter
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2132C>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.895C>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: stop_gained
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.745C>T
  hgvsp: ENSP00000389888.2:p.Arg249Ter
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2132C>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: stop_gained
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.871C>T
  hgvsp: ENSP00000379886.3:p.Arg291Ter
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: stop_gained
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.871C>T
  hgvsp: ENSP00000387430.1:p.Arg291Ter
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: stop gained
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 10079
  bin: 3.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 195
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 28
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 388
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 51
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17604
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 46
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 584
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29401
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 109
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1596
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 76
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 365
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 59
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 17
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1664
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 26
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1615
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10
  bin: 4.25e1
  variant carriers: 0
hgvs: p.Arg291Ter
num of homozygotes: 0
population: East Asian
population: European (Non-Finnish)
population: South Asian
population: African
population: Latino
population: European (Finnish)
population: Other
reference allele: G
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: VQSLOD
site quality: MQ
site quality: FS
site quality: DP
site quality: QD
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: ReadPosRankSum

3-25781080-T-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781080
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781080
    reference: chr 3
allele count: 33
allele frequency: 2.720348204570185e-4
allele num: 121308
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2134A>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.869A>G
  hgvsp: ENSP00000387430.1:p.Asn290Ser
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.743A>G
  hgvsp: ENSP00000389888.2:p.Asn248Ser
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.860A>G
  hgvsp: ENSP00000307980.5:p.Asn287Ser
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.869A>G
  hgvsp: ENSP00000379886.3:p.Asn290Ser
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.869A>G
  hgvsp: ENSP00000280700.5:p.Asn290Ser
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2134A>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.893A>G
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 19
  bin: 8.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 408
  bin: 9.75e1
  variant carriers: 20
genotype depth: GenotypeDepth
  all individuals: 45
  bin: 7.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 15
  bin: 9.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 42
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 194
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 577
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 108
  bin: 5.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 44
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 367
  bin: 4.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 29410
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 60
  bin: 6.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 30
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 76
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17600
  bin: 2.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1587
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10072
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 23
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1887
  bin: 9.75e1
  variant carriers: 32
genotype quality: GenotypeQuality
  all individuals: 12
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 45526
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 15
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
hgvs: p.Asn290Ser
num of homozygotes: 1
population: East Asian
population: European (Non-Finnish)
population: Latino
population: African
population: South Asian
population: Other
population: European (Finnish)
reference allele: T
site quality: BaseQRankSum
site quality: QD
site quality: FS
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: ClippingRankSum
site quality: DP
site quality: MQ
site quality: ReadPosRankSum

3-25781085-G-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781085
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781085
    reference: chr 3
allele count: 2
allele frequency: 1.648505629646725e-5
allele num: 121322
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.864C>G
  hgvsp: ENSP00000387430.1:p.Phe288Leu
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.855C>G
  hgvsp: ENSP00000307980.5:p.Phe285Leu
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.888C>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.864C>G
  hgvsp: ENSP00000379886.3:p.Phe288Leu
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2139C>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2139C>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.738C>G
  hgvsp: ENSP00000389888.2:p.Phe246Leu
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.864C>G
  hgvsp: ENSP00000280700.5:p.Phe288Leu
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: missense
filter: VQSRTrancheSNP99.60to99.80
genotype depth: GenotypeDepth
  all individuals: 31
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 77
  bin: 6.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 27
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 107
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 578
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 194
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10090
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1590
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 388
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 365
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 2
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17595
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29446
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 59
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14
  bin: 9.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 45558
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 20
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1855
  bin: 9.75e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 1664
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 20
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 14
  bin: 4.75e1
  variant carriers: 0
hgvs: p.Phe288Leu
num of homozygotes: 0
population: Latino
population: East Asian
population: European (Finnish)
population: European (Non-Finnish)
population: Other
population: African
population: South Asian
reference allele: G
site quality: VQSLOD
site quality: MQRankSum
site quality: FS
site quality: InbreedingCoeff
site quality: QD
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: DP
site quality: MQ

3-25781107-TG-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781107
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781106
    reference: chr 3
allele count: 4
allele frequency: 3.295653033648617e-5
allele num: 121372
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: frameshift_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.715delC
  hgvsp: ENSP00000389888.2:p.His239IlefsTer43
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: frameshift_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.841delC
  hgvsp: ENSP00000379886.3:p.His281IlefsTer43
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: frameshift_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.841delC
  hgvsp: ENSP00000387430.1:p.His281IlefsTer43
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2162delC
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.865delC
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2162delC
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: frameshift_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.832delC
  hgvsp: ENSP00000307980.5:p.His278IlefsTer43
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: frameshift_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.841delC
  hgvsp: ENSP00000280700.5:p.His281IlefsTer43
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: frameshift
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 195
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 76
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1591
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 578
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 364
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 106
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10106
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17571
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 59
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29500
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 392
  bin: 9.75e1
  variant carriers: 4
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 405
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 330
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1856
  bin: 9.75e1
  variant carriers: 4
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 4.75e1
  variant carriers: 0
hgvs: p.His281IlefsTer43
num of homozygotes: 0
population: Latino
population: East Asian
population: European (Non-Finnish)
population: South Asian
population: Other
population: European (Finnish)
population: African
reference allele: TG
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: MQ
site quality: MQRankSum
site quality: DP
site quality: QD
site quality: FS
site quality: VQSLOD

3-25781108-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781108
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781108
    reference: chr 3
allele count: 3
allele frequency: 2.472065658063878e-5
allele num: 121356
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2162C>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.841C>T
  hgvsp: ENSP00000280700.5:p.His281Tyr
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.865C>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2162C>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.832C>T
  hgvsp: ENSP00000307980.5:p.His278Tyr
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.841C>T
  hgvsp: ENSP00000379886.3:p.His281Tyr
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.715C>T
  hgvsp: ENSP00000389888.2:p.His239Tyr
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.841C>T
  hgvsp: ENSP00000387430.1:p.His281Tyr
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 106
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17569
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 578
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 362
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 196
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10105
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29502
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 390
  bin: 9.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 77
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1592
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 59
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 45630
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8288
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 3.25e1
  variant carriers: 0
hgvs: p.His281Tyr
num of homozygotes: 0
population: European (Finnish)
population: South Asian
population: European (Non-Finnish)
population: Latino
population: African
population: East Asian
population: Other
reference allele: G
site quality: DP
site quality: BaseQRankSum
site quality: VQSLOD
site quality: MQ
site quality: MQRankSum
site quality: FS
site quality: QD
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: ReadPosRankSum

3-25781108-G-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781108
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781108
    reference: chr 3
allele count: 1
allele frequency: 8.240218860212928e-6
allele num: 121356
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2162C>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.841C>G
  hgvsp: ENSP00000379886.3:p.His281Asp
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.865C>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.841C>G
  hgvsp: ENSP00000280700.5:p.His281Asp
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.841C>G
  hgvsp: ENSP00000387430.1:p.His281Asp
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.832C>G
  hgvsp: ENSP00000307980.5:p.His278Asp
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.715C>G
  hgvsp: ENSP00000389888.2:p.His239Asp
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2162C>G
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 578
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29502
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 77
  bin: 6.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 10105
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 362
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1592
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 106
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17569
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 390
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 59
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 196
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1610
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 45630
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 2.5e0
  variant carriers: 0
hgvs: p.His281Asp
num of homozygotes: 0
population: South Asian
population: European (Finnish)
population: East Asian
population: European (Non-Finnish)
population: African
population: Latino
population: Other
reference allele: G
site quality: FS
site quality: DP
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: QD
site quality: MQRankSum
site quality: MQ
site quality: VQSLOD
site quality: ReadPosRankSum

3-25781111-C-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781111
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781111
    reference: chr 3
allele count: 1
allele frequency: 8.239132584121543e-6
allele num: 121372
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.838G>C
  hgvsp: ENSP00000387430.1:p.Asp280His
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2165G>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.829G>C
  hgvsp: ENSP00000307980.5:p.Asp277His
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.712G>C
  hgvsp: ENSP00000389888.2:p.Asp238His
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.838G>C
  hgvsp: ENSP00000379886.3:p.Asp280His
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2165G>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.838G>C
  hgvsp: ENSP00000280700.5:p.Asp280His
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.862G>C
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1590
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10105
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 362
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 76
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17566
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 388
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29514
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 194
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 579
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 107
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 61
  bin: 6.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8298
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 45623
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1668
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 405
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 329
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 19
  bin: 2.25e1
  variant carriers: 0
hgvs: p.Asp280His
num of homozygotes: 0
population: Other
population: African
population: Latino
population: European (Finnish)
population: East Asian
population: South Asian
population: European (Non-Finnish)
reference allele: C
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: VQSLOD
site quality: MQ
site quality: DP
site quality: BaseQRankSum
site quality: QD
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: FS

3-25781119-TC-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781119
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781118
    reference: chr 3
allele count: 1
allele frequency: 8.238182327451271e-6
allele num: 121386
alternate allele: T
annotation: Annotation
  canonical: true
  consequence: frameshift_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.829delG
  hgvsp: ENSP00000280700.5:p.Glu277LysfsTer47
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2174delG
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: frameshift_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.829delG
  hgvsp: ENSP00000379886.3:p.Glu277LysfsTer47
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: frameshift_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.829delG
  hgvsp: ENSP00000387430.1:p.Glu277LysfsTer47
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.853delG
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2174delG
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: frameshift_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.703delG
  hgvsp: ENSP00000389888.2:p.Glu235LysfsTer47
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: frameshift_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.820delG
  hgvsp: ENSP00000307980.5:p.Glu274LysfsTer47
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: frameshift
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 362
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 12
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 578
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 59
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17566
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 107
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 389
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1591
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10107
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 193
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 76
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29522
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1665
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 405
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8300
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 7.5e0
  variant carriers: 0
hgvs: p.Glu277LysfsTer47
num of homozygotes: 0
population: European (Non-Finnish)
population: European (Finnish)
population: Latino
population: African
population: Other
population: East Asian
population: South Asian
reference allele: TC
site quality: FS
site quality: VQSLOD
site quality: QD
site quality: MQRankSum
site quality: MQ
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: DP
site quality: ReadPosRankSum

3-25781126-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781126
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781126
    reference: chr 3
allele count: 5
allele frequency: 4.118887570844866e-5
allele num: 121392
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2180G>A
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.847G>A
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.823G>A
  hgvsp: ENSP00000379886.3:p.Ala275Thr
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.814G>A
  hgvsp: ENSP00000307980.5:p.Ala272Thr
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2180G>A
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.823G>A
  hgvsp: ENSP00000280700.5:p.Ala275Thr
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.697G>A
  hgvsp: ENSP00000389888.2:p.Ala233Thr
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.823G>A
  hgvsp: ENSP00000387430.1:p.Ala275Thr
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 18
  bin: 8.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 361
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 59
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 578
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10102
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17562
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29527
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1593
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 392
  bin: 9.75e1
  variant carriers: 4
genotype depth: GenotypeDepth
  all individuals: 193
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 106
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 76
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 848
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1662
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 329
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 1.75e1
  variant carriers: 0
hgvs: p.Ala275Thr
num of homozygotes: 0
population: Other
population: African
population: European (Non-Finnish)
population: European (Finnish)
population: Latino
population: East Asian
population: South Asian
reference allele: C
site quality: VQSLOD
site quality: MQRankSum
site quality: QD
site quality: FS
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: MQ
site quality: DP

3-25781131-C-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781131
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781131
    reference: chr 3
allele count: 14
allele frequency: 1.153250518962734e-4
allele num: 121396
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.809G>C
  hgvsp: ENSP00000307980.5:p.Trp270Ser
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2185G>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.818G>C
  hgvsp: ENSP00000387430.1:p.Trp273Ser
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.692G>C
  hgvsp: ENSP00000389888.2:p.Trp231Ser
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2185G>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.842G>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.818G>C
  hgvsp: ENSP00000379886.3:p.Trp273Ser
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.818G>C
  hgvsp: ENSP00000280700.5:p.Trp273Ser
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 33
  bin: 7.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 14
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 575
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 76
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17560
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29531
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1590
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 59
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 400
  bin: 9.75e1
  variant carriers: 12
genotype depth: GenotypeDepth
  all individuals: 18
  bin: 8.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 360
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 193
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 104
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10102
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8303
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 45652
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 14
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  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
hgvs: p.Trp273Ser
num of homozygotes: 0
population: South Asian
population: African
population: European (Finnish)
population: European (Non-Finnish)
population: Other
population: East Asian
population: Latino
reference allele: C
site quality: FS
site quality: InbreedingCoeff
site quality: DP
site quality: MQRankSum
site quality: VQSLOD
site quality: ReadPosRankSum
site quality: MQ
site quality: QD
site quality: ClippingRankSum
site quality: BaseQRankSum

3-25781142-A-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781142
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781142
    reference: chr 3
allele count: 1
allele frequency: 8.237910865804433e-6
allele num: 121390
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.681T>A
  hgvsp: ENSP00000389888.2:p.Asp227Glu
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.807T>A
  hgvsp: ENSP00000280700.5:p.Asp269Glu
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.807T>A
  hgvsp: ENSP00000379886.3:p.Asp269Glu
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.807T>A
  hgvsp: ENSP00000387430.1:p.Asp269Glu
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2196T>A
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2196T>A
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.798T>A
  hgvsp: ENSP00000307980.5:p.Asp266Glu
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.831T>A
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 9
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 360
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 577
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 193
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 104
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17559
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 388
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 76
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 59
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1590
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10105
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29547
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 44
  bin: 7.25e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1662
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 846
  bin: 8.25e1
  variant carriers: 0
hgvs: p.Asp269Glu
num of homozygotes: 0
population: East Asian
population: Other
population: African
population: European (Non-Finnish)
population: Latino
population: European (Finnish)
population: South Asian
reference allele: A
site quality: MQRankSum
site quality: BaseQRankSum
site quality: MQ
site quality: ReadPosRankSum
site quality: DP
site quality: QD
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: FS
site quality: ClippingRankSum

http://identifiers.org/exac.variant/3-25781149-C-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781149
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781149
    reference: chr 3
allele count: 3
allele frequency: 2.47133254250692e-5
allele num: 121392
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.800G>T
  hgvsp: ENSP00000379886.3:p.Ser267Ile
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.791G>T
  hgvsp: ENSP00000307980.5:p.Ser264Ile
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2203G>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.824G>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2203G>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.800G>T
  hgvsp: ENSP00000280700.5:p.Ser267Ile
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.800G>T
  hgvsp: ENSP00000387430.1:p.Ser267Ile
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.674G>T
  hgvsp: ENSP00000389888.2:p.Ser225Ile
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 17563
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 361
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10106
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 75
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 193
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 577
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 59
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1591
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 391
  bin: 9.75e1
  variant carriers: 3
genotype depth: GenotypeDepth
  all individuals: 29542
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 104
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1661
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 405
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12
  bin: 2.25e1
  variant carriers: 0
hgvs: p.Ser267Ile
num of homozygotes: 0
population: European (Finnish)
population: Other
population: East Asian
population: African
population: South Asian
population: European (Non-Finnish)
population: Latino
reference allele: C
site quality: MQRankSum
site quality: FS
site quality: ReadPosRankSum
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: DP
site quality: ClippingRankSum
site quality: VQSLOD
site quality: MQ
site quality: QD

3-25781154-C-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781154
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781154
    reference: chr 3
allele count: 1
allele frequency: 8.237775141689733e-6
allele num: 121392
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.795G>C
  hgvsp: ENST00000428257.1:c.795G>C(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2208G>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.786G>C
  hgvsp: ENST00000308710.5:c.786G>C(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.819G>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.669G>C
  hgvsp: ENST00000417874.2:c.669G>C(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.795G>C
  hgvsp: ENST00000396649.3:c.795G>C(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2208G>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.795G>C
  hgvsp: ENST00000280700.5:c.795G>C(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1594
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 104
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 362
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 194
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10105
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29552
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 574
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17553
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 59
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 389
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 75
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 10
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 45674
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8306
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6
  bin: 2.75e1
  variant carriers: 0
hgvs: p.Leu265Leu
num of homozygotes: 0
population: European (Non-Finnish)
population: European (Finnish)
population: Other
population: Latino
population: East Asian
population: African
population: South Asian
reference allele: C
site quality: FS
site quality: VQSLOD
site quality: MQ
site quality: QD
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: DP
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: ReadPosRankSum

http://identifiers.org/exac.variant/3-25781155-A-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781155
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781155
    reference: chr 3
allele count: 1
allele frequency: 8.237639422047218e-6
allele num: 121394
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2209T>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.668T>G
  hgvsp: ENSP00000389888.2:p.Leu223Arg
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.794T>G
  hgvsp: ENSP00000387430.1:p.Leu265Arg
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.794T>G
  hgvsp: ENSP00000280700.5:p.Leu265Arg
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2209T>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.794T>G
  hgvsp: ENSP00000379886.3:p.Leu265Arg
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.785T>G
  hgvsp: ENSP00000307980.5:p.Leu262Arg
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.818T>G
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 572
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17555
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10106
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1594
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 75
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29553
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 194
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 59
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 361
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 104
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 390
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1663
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1612
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
hgvs: p.Leu265Arg
num of homozygotes: 0
population: African
population: East Asian
population: Other
population: European (Non-Finnish)
population: South Asian
population: Latino
population: European (Finnish)
reference allele: A
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: DP
site quality: FS
site quality: BaseQRankSum
site quality: QD
site quality: MQRankSum
site quality: MQ
site quality: ReadPosRankSum
site quality: VQSLOD

3-25781155-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781155
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781155
    reference: chr 3
allele count: 1
allele frequency: 8.237639422047218e-6
allele num: 121394
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.668T>C
  hgvsp: ENSP00000389888.2:p.Leu223Pro
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.794T>C
  hgvsp: ENSP00000280700.5:p.Leu265Pro
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.785T>C
  hgvsp: ENSP00000307980.5:p.Leu262Pro
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2209T>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.794T>C
  hgvsp: ENSP00000387430.1:p.Leu265Pro
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.818T>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.794T>C
  hgvsp: ENSP00000379886.3:p.Leu265Pro
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2209T>C
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 17555
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1594
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29553
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 59
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 75
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10106
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 5
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 104
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 572
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 194
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 361
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 390
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 844
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 45678
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 404
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1663
  bin: 7.25e1
  variant carriers: 0
hgvs: p.Leu265Pro
num of homozygotes: 0
population: South Asian
population: European (Non-Finnish)
population: Other
population: Latino
population: African
population: European (Finnish)
population: East Asian
reference allele: A
site quality: BaseQRankSum
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: QD
site quality: FS
site quality: ClippingRankSum
site quality: MQ
site quality: VQSLOD
site quality: DP
site quality: InbreedingCoeff

3-25781161-G-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781161
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781161
    reference: chr 3
allele count: 1
allele frequency: 8.237639422047218e-6
allele num: 121394
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: stop_gained
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.662C>A
  hgvsp: ENSP00000389888.2:p.Ser221Ter
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: stop_gained
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.779C>A
  hgvsp: ENSP00000307980.5:p.Ser260Ter
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: stop_gained
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.788C>A
  hgvsp: ENSP00000280700.5:p.Ser263Ter
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: stop_gained
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.788C>A
  hgvsp: ENSP00000379886.3:p.Ser263Ter
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2215C>A
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: stop_gained
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.788C>A
  hgvsp: ENSP00000387430.1:p.Ser263Ter
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2215C>A
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.812C>A
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: stop gained
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 59
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 75
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 194
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 389
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 29561
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 573
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1592
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10105
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17551
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 359
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 104
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1834
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 5.25e1
  variant carriers: 0
hgvs: p.Ser263Ter
num of homozygotes: 0
population: Other
population: African
population: European (Non-Finnish)
population: East Asian
population: Latino
population: South Asian
population: European (Finnish)
reference allele: G
site quality: BaseQRankSum
site quality: FS
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: QD
site quality: ClippingRankSum
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: DP
site quality: MQ

3-25781166-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781166
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781166
    reference: chr 3
allele count: 2
allele frequency: 1.647582173160887e-5
allele num: 121390
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.807T>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2220T>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.783T>C
  hgvsp: ENST00000280700.5:c.783T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.783T>C
  hgvsp: ENST00000396649.3:c.783T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2220T>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.657T>C
  hgvsp: ENST00000417874.2:c.657T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.774T>C
  hgvsp: ENST00000308710.5:c.774T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.783T>C
  hgvsp: ENST00000428257.1:c.783T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 194
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 104
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 573
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 390
  bin: 9.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 1591
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17553
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 59
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 358
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29558
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10104
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 75
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 5.25e1
  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: 0
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 45680
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 16
  bin: 2.25e1
  variant carriers: 0
hgvs: p.Asp261Asp
num of homozygotes: 0
population: African
population: South Asian
population: Latino
population: European (Non-Finnish)
population: European (Finnish)
population: East Asian
population: Other
reference allele: A
site quality: DP
site quality: ReadPosRankSum
site quality: VQSLOD
site quality: ClippingRankSum
site quality: InbreedingCoeff
site quality: FS
site quality: MQ
site quality: MQRankSum
site quality: BaseQRankSum
site quality: QD

http://identifiers.org/exac.variant/3-25781178-A-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781178
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781178
    reference: chr 3
allele count: 1
allele frequency: 8.238182327451271e-6
allele num: 121386
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.645T>G
  hgvsp: ENST00000417874.2:c.645T>G(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2232T>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.771T>G
  hgvsp: ENST00000396649.3:c.771T>G(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.771T>G
  hgvsp: ENST00000280700.5:c.771T>G(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.771T>G
  hgvsp: ENST00000428257.1:c.771T>G(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2232T>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.762T>G
  hgvsp: ENST00000308710.5:c.762T>G(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.795T>G
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1592
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 359
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 572
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 75
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 104
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17546
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10105
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29565
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 389
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 192
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 59
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1664
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 327
  bin: 8.75e1
  variant carriers: 0
hgvs: p.Thr257Thr
num of homozygotes: 0
population: European (Finnish)
population: Other
population: African
population: Latino
population: European (Non-Finnish)
population: East Asian
population: South Asian
reference allele: A
site quality: InbreedingCoeff
site quality: QD
site quality: ClippingRankSum
site quality: MQ
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: VQSLOD
site quality: FS
site quality: BaseQRankSum
site quality: DP

3-25781184-T-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781184
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781184
    reference: chr 3
allele count: 1
allele frequency: 8.238453806989504e-6
allele num: 121382
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2238A>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.756A>G
  hgvsp: ENST00000308710.5:c.756A>G(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.639A>G
  hgvsp: ENST00000417874.2:c.639A>G(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.765A>G
  hgvsp: ENST00000428257.1:c.765A>G(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.789A>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.765A>G
  hgvsp: ENST00000396649.3:c.765A>G(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.765A>G
  hgvsp: ENST00000280700.5:c.765A>G(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2238A>G
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: synonymous
filter: VQSRTrancheSNP99.60to99.80
genotype depth: GenotypeDepth
  all individuals: 17547
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 75
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 192
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 389
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 104
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1591
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29564
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 359
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10105
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 59
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 572
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 20
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1662
  bin: 7.25e1
  variant carriers: 0
hgvs: p.Gly255Gly
num of homozygotes: 0
population: European (Non-Finnish)
population: Latino
population: African
population: Other
population: East Asian
population: South Asian
population: European (Finnish)
reference allele: T
site quality: InbreedingCoeff
site quality: DP
site quality: FS
site quality: BaseQRankSum
site quality: MQRankSum
site quality: ClippingRankSum
site quality: VQSLOD
site quality: MQ
site quality: QD
site quality: ReadPosRankSum

3-25781185-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781185
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781185
    reference: chr 3
allele count: 1
allele frequency: 8.238318064983852e-6
allele num: 121384
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.788G>A
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.764G>A
  hgvsp: ENSP00000379886.3:p.Gly255Glu
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.764G>A
  hgvsp: ENSP00000280700.5:p.Gly255Glu
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.764G>A
  hgvsp: ENSP00000387430.1:p.Gly255Glu
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.755G>A
  hgvsp: ENSP00000307980.5:p.Gly252Glu
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2239G>A
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2239G>A
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.638G>A
  hgvsp: ENSP00000389888.2:p.Gly213Glu
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 17545
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29568
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 572
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 192
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 0
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1591
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 59
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 359
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 6
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 389
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 75
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 104
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10103
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 20
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 845
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1661
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1831
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 4.25e1
  variant carriers: 0
hgvs: p.Gly255Glu
num of homozygotes: 0
population: East Asian
population: European (Finnish)
population: African
population: Other
population: South Asian
population: European (Non-Finnish)
population: Latino
reference allele: C
site quality: BaseQRankSum
site quality: DP
site quality: VQSLOD
site quality: ClippingRankSum
site quality: FS
site quality: InbreedingCoeff
site quality: MQ
site quality: QD
site quality: MQRankSum
site quality: ReadPosRankSum

3-25781188-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781188
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781188
    reference: chr 3
allele count: 2
allele frequency: 1.64766361299677e-5
allele num: 121384
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.635G>A
  hgvsp: ENSP00000389888.2:p.Gly212Asp
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.752G>A
  hgvsp: ENSP00000307980.5:p.Gly251Asp
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.761G>A
  hgvsp: ENSP00000387430.1:p.Gly254Asp
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.761G>A
  hgvsp: ENSP00000280700.5:p.Gly254Asp
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.785G>A
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.761G>A
  hgvsp: ENSP00000379886.3:p.Gly254Asp
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2242G>A
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2242G>A
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 59
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 75
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 390
  bin: 9.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 1589
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 104
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 193
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 573
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17545
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10104
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29565
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 358
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 20
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1832
  bin: 9.75e1
  variant carriers: 2
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 3.75e1
  variant carriers: 0
hgvs: p.Gly254Asp
num of homozygotes: 0
population: European (Non-Finnish)
population: African
population: European (Finnish)
population: Latino
population: East Asian
population: Other
population: South Asian
reference allele: C
site quality: DP
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: MQ
site quality: InbreedingCoeff
site quality: FS
site quality: MQRankSum
site quality: VQSLOD
site quality: ReadPosRankSum
site quality: QD

http://identifiers.org/exac.variant/3-25781191-C-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781191
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781191
    reference: chr 3
allele count: 5
allele frequency: 4.119159032491926e-5
allele num: 121384
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.758G>T
  hgvsp: ENSP00000379886.3:p.Cys253Phe
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.749G>T
  hgvsp: ENSP00000307980.5:p.Cys250Phe
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2245G>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.632G>T
  hgvsp: ENSP00000389888.2:p.Cys211Phe
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.758G>T
  hgvsp: ENSP00000387430.1:p.Cys253Phe
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.782G>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.758G>T
  hgvsp: ENSP00000280700.5:p.Cys253Phe
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2245G>T
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 76
  bin: 6.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1591
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17546
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 358
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 571
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 104
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10101
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29565
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 392
  bin: 9.75e1
  variant carriers: 4
genotype depth: GenotypeDepth
  all individuals: 191
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 59
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 20
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 842
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 45682
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 5.75e1
  variant carriers: 0
hgvs: p.Cys253Phe
num of homozygotes: 0
population: South Asian
population: Latino
population: European (Non-Finnish)
population: African
population: European (Finnish)
population: Other
population: East Asian
reference allele: C
site quality: FS
site quality: ReadPosRankSum
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: MQ
site quality: ClippingRankSum
site quality: QD
site quality: VQSLOD
site quality: MQRankSum
site quality: DP

3-25781199-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781199
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781199
    reference: chr 3
allele count: 1
allele frequency: 8.238589553468446e-6
allele num: 121380
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.741C>T
  hgvsp: ENST00000308710.5:c.741C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.750C>T
  hgvsp: ENST00000396649.3:c.750C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.774C>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2253C>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.624C>T
  hgvsp: ENST00000417874.2:c.624C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2253C>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.750C>T
  hgvsp: ENST00000428257.1:c.750C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.750C>T
  hgvsp: ENST00000280700.5:c.750C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 357
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17544
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29568
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 8
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 14
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 389
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1591
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 191
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10103
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 75
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 104
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 570
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 31
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 59
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1663
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 842
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 45685
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1828
  bin: 9.75e1
  variant carriers: 1
hgvs: p.Cys250Cys
num of homozygotes: 0
population: Other
population: European (Finnish)
population: East Asian
population: European (Non-Finnish)
population: African
population: South Asian
population: Latino
reference allele: G
site quality: FS
site quality: ClippingRankSum
site quality: MQ
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: MQRankSum
site quality: BaseQRankSum
site quality: QD
site quality: ReadPosRankSum
site quality: DP

3-25781206-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781206
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781206
    reference: chr 3
allele count: 1
allele frequency: 8.239404126293587e-6
allele num: 121368
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.743T>C
  hgvsp: ENSP00000387430.1:p.Val248Ala
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.767T>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.734T>C
  hgvsp: ENSP00000307980.5:p.Val245Ala
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.743T>C
  hgvsp: ENSP00000280700.5:p.Val248Ala
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.617T>C
  hgvsp: ENSP00000389888.2:p.Val206Ala
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.743T>C
  hgvsp: ENSP00000379886.3:p.Val248Ala
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2260T>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2260T>C
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10102
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 104
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 572
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29558
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 60
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 191
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 388
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 356
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18
  bin: 8.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 17544
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 75
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 31
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1589
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1605
  bin: 7.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 403
  bin: 9.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 327
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.75e1
  variant carriers: 0
hgvs: p.Val248Ala
num of homozygotes: 0
population: African
population: European (Non-Finnish)
population: East Asian
population: European (Finnish)
population: South Asian
population: Latino
population: Other
reference allele: A
site quality: QD
site quality: VQSLOD
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: FS
site quality: BaseQRankSum
site quality: MQ
site quality: DP
site quality: InbreedingCoeff
site quality: ClippingRankSum

3-25781208-G-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781208
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781208
    reference: chr 3
allele count: 15
allele frequency: 1.235951352954748e-4
allele num: 121364
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2262C>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.732C>T
  hgvsp: ENST00000308710.5:c.732C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.741C>T
  hgvsp: ENST00000428257.1:c.741C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.741C>T
  hgvsp: ENST00000280700.5:c.741C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.741C>T
  hgvsp: ENST00000396649.3:c.741C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2262C>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.615C>T
  hgvsp: ENST00000417874.2:c.615C>T(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.765C>T
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 190
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29553
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 44
  bin: 7.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 18
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1587
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 57
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 569
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 31
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 400
  bin: 9.75e1
  variant carriers: 12
genotype depth: GenotypeDepth
  all individuals: 354
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10104
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17542
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 104
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 19
  bin: 8.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 75
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 841
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 45675
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 3
  bin: 4.25e1
  variant carriers: 0
hgvs: p.Asn247Asn
num of homozygotes: 0
population: European (Non-Finnish)
population: East Asian
population: African
population: Latino
population: Other
population: European (Finnish)
population: South Asian
reference allele: G
site quality: InbreedingCoeff
site quality: DP
site quality: BaseQRankSum
site quality: ReadPosRankSum
site quality: MQ
site quality: ClippingRankSum
site quality: VQSLOD
site quality: MQRankSum
site quality: FS
site quality: QD

3-25781209-T-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781209
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781209
    reference: chr 3
allele count: 1
allele frequency: 8.239268352970255e-6
allele num: 121370
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.740A>G
  hgvsp: ENSP00000379886.3:p.Asn247Ser
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.614A>G
  hgvsp: ENSP00000389888.2:p.Asn205Ser
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.764A>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.740A>G
  hgvsp: ENSP00000387430.1:p.Asn247Ser
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.731A>G
  hgvsp: ENSP00000307980.5:p.Asn244Ser
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2263A>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2263A>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.740A>G
  hgvsp: ENSP00000280700.5:p.Asn247Ser
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 75
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 569
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17546
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 104
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10107
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 354
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 11
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1588
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29559
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 57
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 389
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 31
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 190
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1820
  bin: 9.75e1
  variant carriers: 1
hgvs: p.Asn247Ser
num of homozygotes: 0
population: Latino
population: African
population: European (Non-Finnish)
population: South Asian
population: Other
population: East Asian
population: European (Finnish)
reference allele: T
site quality: VQSLOD
site quality: ClippingRankSum
site quality: DP
site quality: InbreedingCoeff
site quality: MQ
site quality: BaseQRankSum
site quality: QD
site quality: MQRankSum
site quality: FS
site quality: ReadPosRankSum

3-25781213-T-A
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781213
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781213
    reference: chr 3
allele count: 1
allele frequency: 8.239811473113496e-6
allele num: 121362
alternate allele: A
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.736A>T
  hgvsp: ENSP00000387430.1:p.Asn246Tyr
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.610A>T
  hgvsp: ENSP00000389888.2:p.Asn204Tyr
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.736A>T
  hgvsp: ENSP00000379886.3:p.Asn246Tyr
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.727A>T
  hgvsp: ENSP00000307980.5:p.Asn243Tyr
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.736A>T
  hgvsp: ENSP00000280700.5:p.Asn246Tyr
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2267A>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.760A>T
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2267A>T
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 389
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 29559
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 75
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 190
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 104
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 57
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1587
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17541
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 568
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 20
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10109
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 354
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 31
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 31
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 403
  bin: 9.25e1
  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: 6
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 1.75e1
  variant carriers: 0
hgvs: p.Asn246Tyr
num of homozygotes: 0
population: South Asian
population: European (Finnish)
population: East Asian
population: Latino
population: African
population: European (Non-Finnish)
population: Other
reference allele: T
site quality: VQSLOD
site quality: MQRankSum
site quality: DP
site quality: ReadPosRankSum
site quality: QD
site quality: BaseQRankSum
site quality: MQ
site quality: FS
site quality: ClippingRankSum
site quality: InbreedingCoeff

3-25781220-G-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781220
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781220
    reference: chr 3
allele count: 2
allele frequency: 1.648288252649623e-5
allele num: 121338
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2274C>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.753C>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2274C>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.720C>G
  hgvsp: ENSP00000307980.5:p.His240Gln
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.729C>G
  hgvsp: ENSP00000280700.5:p.His243Gln
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.729C>G
  hgvsp: ENSP00000387430.1:p.His243Gln
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.729C>G
  hgvsp: ENSP00000379886.3:p.His243Gln
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.603C>G
  hgvsp: ENSP00000389888.2:p.His201Gln
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 57
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 355
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 570
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 26
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29558
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 189
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 31
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 23
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 75
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18
  bin: 8.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1587
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 389
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 104
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10108
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17532
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 840
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 40
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 5.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 4.25e1
  variant carriers: 0
hgvs: p.His243Gln
num of homozygotes: 0
population: European (Non-Finnish)
population: African
population: East Asian
population: Other
population: European (Finnish)
population: Latino
population: South Asian
reference allele: G
site quality: InbreedingCoeff
site quality: MQRankSum
site quality: VQSLOD
site quality: MQ
site quality: FS
site quality: BaseQRankSum
site quality: ClippingRankSum
site quality: QD
site quality: DP
site quality: ReadPosRankSum

3-25781232-T-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781232
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781232
    reference: chr 3
allele count: 2
allele frequency: 1.648804616652927e-5
allele num: 121300
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.741A>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.717A>C
  hgvsp: ENSP00000280700.5:p.Glu239Asp
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2286A>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.717A>C
  hgvsp: ENSP00000387430.1:p.Glu239Asp
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2286A>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.717A>C
  hgvsp: ENSP00000379886.3:p.Glu239Asp
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.591A>C
  hgvsp: ENSP00000389888.2:p.Glu197Asp
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.708A>C
  hgvsp: ENSP00000307980.5:p.Glu236Asp
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 48
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 389
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 354
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 568
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29556
  bin: 2.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 189
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 31
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10106
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 18
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 104
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 57
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 75
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17492
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1586
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 75
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 840
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1658
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2
  bin: 4.25e1
  variant carriers: 0
hgvs: p.Glu239Asp
num of homozygotes: 0
population: East Asian
population: Latino
population: South Asian
population: African
population: Other
population: European (Non-Finnish)
population: European (Finnish)
reference allele: T
site quality: VQSLOD
site quality: MQRankSum
site quality: MQ
site quality: QD
site quality: InbreedingCoeff
site quality: FS
site quality: DP
site quality: ReadPosRankSum
site quality: BaseQRankSum
site quality: ClippingRankSum

3-25781235-C-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781235
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781235
    reference: chr 3
allele count: 1
allele frequency: 8.245110649384915e-6
allele num: 121284
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.738G>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.714G>C
  hgvsp: ENSP00000379886.3:p.Lys238Asn
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.714G>C
  hgvsp: ENSP00000280700.5:p.Lys238Asn
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.714G>C
  hgvsp: ENSP00000387430.1:p.Lys238Asn
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2289G>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.588G>C
  hgvsp: ENSP00000389888.2:p.Lys196Asn
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.705G>C
  hgvsp: ENSP00000307980.5:p.Lys235Asn
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2289G>C
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 189
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 50
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 21
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29554
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 54
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1588
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 31
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 4
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17472
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 76
  bin: 6.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 104
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 355
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 567
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 388
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10107
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 57
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 14
  bin: 3.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1819
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 1656
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 0
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 4.75e1
  variant carriers: 0
hgvs: p.Lys238Asn
num of homozygotes: 0
population: European (Finnish)
population: Latino
population: East Asian
population: European (Non-Finnish)
population: Other
population: African
population: South Asian
reference allele: C
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: DP
site quality: MQ
site quality: VQSLOD
site quality: InbreedingCoeff
site quality: ClippingRankSum
site quality: FS
site quality: QD
site quality: BaseQRankSum

3-25781245-T-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781245
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781245
    reference: chr 3
allele count: 1
allele frequency: 8.253276550790664e-6
allele num: 121164
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2299A>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.578A>G
  hgvsp: ENSP00000389888.2:p.His193Arg
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.728A>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.704A>G
  hgvsp: ENSP00000379886.3:p.His235Arg
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.704A>G
  hgvsp: ENSP00000387430.1:p.His235Arg
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.695A>G
  hgvsp: ENSP00000307980.5:p.His232Arg
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.704A>G
  hgvsp: ENSP00000280700.5:p.His235Arg
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2299A>G
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1585
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 113
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29511
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 104
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 31
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 126
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 75
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 189
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 565
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10091
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 354
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 57
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 7
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17389
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 31
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 388
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.25e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 9
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 45476
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 202
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 4
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1596
  bin: 7.75e1
  variant carriers: 0
hgvs: p.His235Arg
num of homozygotes: 0
population: African
population: European (Non-Finnish)
population: Latino
population: Other
population: South Asian
population: East Asian
population: European (Finnish)
reference allele: T
site quality: MQ
site quality: BaseQRankSum
site quality: VQSLOD
site quality: QD
site quality: ReadPosRankSum
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: FS
site quality: DP
site quality: ClippingRankSum

3-25781257-A-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781257
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781257
    reference: chr 3
allele count: 1
allele frequency: 8.276775368316504e-6
allele num: 120820
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.692T>A
  hgvsp: ENSP00000379886.3:p.Leu231Gln
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.692T>A
  hgvsp: ENSP00000280700.5:p.Leu231Gln
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2311T>A
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.692T>A
  hgvsp: ENSP00000387430.1:p.Leu231Gln
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.566T>A
  hgvsp: ENSP00000389888.2:p.Leu189Gln
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2311T>A
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.683T>A
  hgvsp: ENSP00000307980.5:p.Leu228Gln
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.716T>A
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 31
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 283
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 190
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 104
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 272
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 355
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17153
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 69
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10045
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 57
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 565
  bin: 4.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 75
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 388
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1578
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29437
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 495
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 11
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 20
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 5
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 36
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 834
  bin: 8.25e1
  variant carriers: 0
hgvs: p.Leu231Gln
num of homozygotes: 0
population: South Asian
population: African
population: Other
population: European (Non-Finnish)
population: European (Finnish)
population: Latino
population: East Asian
reference allele: A
site quality: MQ
site quality: ReadPosRankSum
site quality: QD
site quality: FS
site quality: VQSLOD
site quality: DP
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: BaseQRankSum
site quality: ClippingRankSum

3-25781261-A-G
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781261
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781261
    reference: chr 3
allele count: 1
allele frequency: 8.282670995742708e-6
allele num: 120734
alternate allele: G
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.688T>C
  hgvsp: ENST00000428257.1:c.688T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.562T>C
  hgvsp: ENST00000417874.2:c.562T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2315T>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.712T>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.688T>C
  hgvsp: ENST00000280700.5:c.688T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.679T>C
  hgvsp: ENST00000308710.5:c.679T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2315T>C
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: synonymous_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.688T>C
  hgvsp: ENST00000396649.3:c.688T>C(p.%3D)
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: synonymous
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 17064
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 29429
  bin: 2.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 311
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1579
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 564
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 81
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 19
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 189
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 388
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 10039
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 332
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 75
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 104
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 354
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 31
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 58
  bin: 6.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 17
  bin: 4.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 7
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 6
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 8189
  bin: 6.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 833
  bin: 8.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 45091
  bin: 6.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 44
  bin: 2.75e1
  variant carriers: 0
hgvs: p.Leu230Leu
num of homozygotes: 0
population: Other
population: European (Non-Finnish)
population: African
population: European (Finnish)
population: East Asian
population: South Asian
population: Latino
reference allele: A
site quality: VQSLOD
site quality: ReadPosRankSum
site quality: ClippingRankSum
site quality: BaseQRankSum
site quality: InbreedingCoeff
site quality: FS
site quality: MQRankSum
site quality: DP
site quality: QD
site quality: MQ

3-25781278-C-T
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781278
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781278
    reference: chr 3
allele count: 1
allele frequency: 8.373105584861425e-6
allele num: 119430
alternate allele: T
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.695G>A
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.671G>A
  hgvsp: ENSP00000387430.1:p.Ser224Asn
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2332G>A
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2332G>A
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.662G>A
  hgvsp: ENSP00000307980.5:p.Ser221Asn
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.671G>A
  hgvsp: ENSP00000379886.3:p.Ser224Asn
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.545G>A
  hgvsp: ENSP00000389888.2:p.Ser182Asn
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.671G>A
  hgvsp: ENSP00000280700.5:p.Ser224Asn
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 105
  bin: 5.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 867
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1555
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1154
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 57
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 560
  bin: 4.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 188
  bin: 5.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 352
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 89
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 267
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16058
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 31
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 74
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9876
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 388
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 28991
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 1806
  bin: 9.75e1
  variant carriers: 1
genotype quality: GenotypeQuality
  all individuals: 45
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 12
  bin: 2.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 128
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 19
  bin: 1.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 104
  bin: 7.5e0
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 318
  bin: 8.75e1
  variant carriers: 0
hgvs: p.Ser224Asn
num of homozygotes: 0
population: South Asian
population: European (Non-Finnish)
population: East Asian
population: European (Finnish)
population: Latino
population: African
population: Other
reference allele: C
site quality: VQSLOD
site quality: ReadPosRankSum
site quality: BaseQRankSum
site quality: FS
site quality: MQ
site quality: MQRankSum
site quality: InbreedingCoeff
site quality: DP
site quality: QD
site quality: ClippingRankSum

3-25781282-T-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781282
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781282
    reference: chr 3
allele count: 10
allele frequency: 8.417650128790047e-5
allele num: 118798
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2336A>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.691A>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.667A>G
  hgvsp: ENSP00000387430.1:p.Ile223Val
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.541A>G
  hgvsp: ENSP00000389888.2:p.Ile181Val
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2336A>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.667A>G
  hgvsp: ENSP00000379886.3:p.Ile223Val
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.658A>G
  hgvsp: ENSP00000307980.5:p.Ile220Val
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.667A>G
  hgvsp: ENSP00000280700.5:p.Ile223Val
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 385
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 388
  bin: 9.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1647
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 187
  bin: 5.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 1543
  bin: 3.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 32
  bin: 7.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 351
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 555
  bin: 4.25e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 15652
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1138
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 28603
  bin: 2.75e1
  variant carriers: 2
genotype depth: GenotypeDepth
  all individuals: 127
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 107
  bin: 5.75e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 57
  bin: 6.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 74
  bin: 6.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 9763
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 66
  bin: 4.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 185
  bin: 5.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 15
  bin: 1.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 2261
  bin: 2.25e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 168
  bin: 3.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 331
  bin: 2.75e1
  variant carriers: 0
genotype quality: GenotypeQuality
  all individuals: 306
  bin: 3.25e1
  variant carriers: 0
hgvs: p.Ile223Val
num of homozygotes: 0
population: Other
population: European (Non-Finnish)
population: European (Finnish)
population: South Asian
population: East Asian
population: Latino
population: African
reference allele: T
site quality: BaseQRankSum
site quality: MQRankSum
site quality: ReadPosRankSum
site quality: InbreedingCoeff
site quality: VQSLOD
site quality: QD
site quality: FS
site quality: ClippingRankSum
site quality: MQ
site quality: DP

3-25781284-T-C
type: Variant
location: Region
  begin: Position
    type: ExactPosition
    position: 25781284
    reference: chr 3
  end: Position
    type: ExactPosition
    position: 25781284
    reference: chr 3
allele count: 1
allele frequency: 8.429570934839416e-6
allele num: 118630
alternate allele: C
annotation: Annotation
  canonical: false
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000395878
  ensembl transcript: ENST00000422724
  gene symbol: NGLY1
  hgvsc: ENST00000422724.2:c.428-2338A>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: non_coding_transcript_variant
  consequence: non_coding_transcript_exon_variant
  ensembl gene: ENSG00000151092
  ensembl transcript: ENST00000493324
  gene symbol: NGLY1
  hgvsc: ENST00000493324.1:n.689A>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: NMD_transcript_variant
  consequence: intron_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280699
  ensembl transcript: ENST00000280699
  gene symbol: NGLY1
  hgvsc: ENST00000280699.9:c.633-2338A>G
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: true
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000280700
  ensembl transcript: ENST00000280700
  gene symbol: NGLY1
  hgvsc: ENST00000280700.5:c.665A>G
  hgvsp: ENSP00000280700.5:p.Asn222Ser
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000389888
  ensembl transcript: ENST00000417874
  gene symbol: NGLY1
  hgvsc: ENST00000417874.2:c.539A>G
  hgvsp: ENSP00000389888.2:p.Asn180Ser
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000307980
  ensembl transcript: ENST00000308710
  gene symbol: NGLY1
  hgvsc: ENST00000308710.5:c.656A>G
  hgvsp: ENSP00000307980.5:p.Asn219Ser
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000379886
  ensembl transcript: ENST00000396649
  gene symbol: NGLY1
  hgvsc: ENST00000396649.3:c.665A>G
  hgvsp: ENSP00000379886.3:p.Asn222Ser
  variant of: http://identifiers.org/hgnc/17646
annotation: Annotation
  canonical: false
  consequence: missense_variant
  ensembl gene: ENSG00000151092
  ensembl protein: ENSP00000387430
  ensembl transcript: ENST00000428257
  gene symbol: NGLY1
  hgvsc: ENST00000428257.1:c.665A>G
  hgvsp: ENSP00000387430.1:p.Asn222Ser
  variant of: http://identifiers.org/hgnc/17646
canonical: true
consequence: missense
filter: PASS
genotype depth: GenotypeDepth
  all individuals: 1215
  bin: 7.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 15558
  bin: 2.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1533
  bin: 3.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 31
  bin: 7.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 428
  bin: 1.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 136
  bin: 2.5e0
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 351
  bin: 4.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 17
  bin: 8.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 9716
  bin: 3.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 551
  bin: 4.25e1
  variant carriers: 1
genotype depth: GenotypeDepth
  all individuals: 73
  bin: 6.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 388
  bin: 9.75e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 16
  bin: 8.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 13
  bin: 9.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 1785
  bin: 1.25e1
  variant carriers: 0
genotype depth: GenotypeDepth
  all individuals: 43
  bin: 7.25e1
  variant carriers: 0
hgvs: p.Asn222Ser
num of homozygotes: 0
reference allele: T

GenotypeQuality
all individuals: 113
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 170
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1202
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 6
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 12
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 113
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 667
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 208
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 605
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 223
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 3640
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 170
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 266
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2031
bin: 9.75e1
variant carriers: 2

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11318
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 884
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6552
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.519064256418047e-5
allele num: 65830
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8562
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: 1
allele frequency: 6.317119393556538e-5
allele num: 15830
num of homozygotes: 0

ReadPosRankSum
type: SiteQuality
SIO_000300: 3.52e-1

QD
type: SiteQuality
SIO_000300: 1.198e1

ClippingRankSum
type: SiteQuality
SIO_000300: -5.24e-1

MQRankSum
type: SiteQuality
SIO_000300: 1.34e0

VQSLOD
type: SiteQuality
SIO_000300: -1.069e0

FS
type: SiteQuality
SIO_000300: 0.0e0

DP
type: SiteQuality
SIO_000300: 1.484536e6

MQ
type: SiteQuality
SIO_000300: 5.673e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.0e-4

BaseQRankSum
type: SiteQuality
SIO_000300: 1.6e0

GenotypeQuality
all individuals: 13
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 161
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 198
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2030
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 1150
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 184
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 101
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 274
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 333
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 670
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 13
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 223
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 3665
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 50552
bin: 6.25e1
variant carriers: 0

African
type: Population
allele count: 1
allele frequency: 9.778994719342852e-5
allele num: 10226
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 884
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11328
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 65872
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 15856
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8562
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6558
num of homozygotes: 0

DP
type: SiteQuality
SIO_000300: 1.485691e6

BaseQRankSum
type: SiteQuality
SIO_000300: -2.387e0

MQRankSum
type: SiteQuality
SIO_000300: 3.52e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 1.32e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.0e-4

MQ
type: SiteQuality
SIO_000300: 5.954e1

ReadPosRankSum
type: SiteQuality
SIO_000300: -1.604e0

FS
type: SiteQuality
SIO_000300: 0.0e0

QD
type: SiteQuality
SIO_000300: 1.243e1

VQSLOD
type: SiteQuality
SIO_000300: -1.162e-1

GenotypeQuality
all individuals: 86
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 65
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 5
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 647
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 3777
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 167
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 34
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 4
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 6
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 91
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 673
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 226
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 615
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 85
bin: 5.75e1
variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8606
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10332
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16212
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11444
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.508386629660915e-5
allele num: 66296
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 892
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6578
num of homozygotes: 0

QD
type: SiteQuality
SIO_000300: 1.457e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.0e-4

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.2e0

FS
type: SiteQuality
SIO_000300: 6.941e0

MQRankSum
type: SiteQuality
SIO_000300: -6.6e-2

MQ
type: SiteQuality
SIO_000300: 5.939e1

VQSLOD
type: SiteQuality
SIO_000300: 2.23e-1

DP
type: SiteQuality
SIO_000300: 1.499874e6

ClippingRankSum
type: SiteQuality
SIO_000300: -1.743e0

BaseQRankSum
type: SiteQuality
SIO_000300: 6.78e-1

GenotypeQuality
all individuals: 6
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 103
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 70
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 57
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 701
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 600
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3818
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 83
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 167
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 225
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 51611
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 667
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 86
bin: 3.25e1
variant carriers: 0

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

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8604
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10332
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66310
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 6.165988407941794e-5
allele num: 16218
num of homozygotes: 0

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

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

ReadPosRankSum
type: SiteQuality
SIO_000300: 5.22e-1

MQ
type: SiteQuality
SIO_000300: 5.937e1

VQSLOD
type: SiteQuality
SIO_000300: 1.06e0

DP
type: SiteQuality
SIO_000300: 1.501562e6

MQRankSum
type: SiteQuality
SIO_000300: 1.39e0

FS
type: SiteQuality
SIO_000300: 0.0e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.0e-4

ClippingRankSum
type: SiteQuality
SIO_000300: 2.19e-1

QD
type: SiteQuality
SIO_000300: 1.047e1

BaseQRankSum
type: SiteQuality
SIO_000300: 1.1e0

GenotypeQuality
all individuals: 7
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 70
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 667
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2035
bin: 9.75e1
variant carriers: 6

GenotypeQuality
all individuals: 57
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 701
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 335
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 83
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 41
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 51611
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 6
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 103
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 167
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 225
bin: 9.25e1
variant carriers: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16218
num of homozygotes: 0

Latino
type: Population
allele count: 3
allele frequency: 2.621919244887258e-4
allele num: 11442
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 9.678668215253581e-5
allele num: 10332
num of homozygotes: 0

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

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

East Asian
type: Population
allele count: 1
allele frequency: 1.162250116225012e-4
allele num: 8604
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.508068164681044e-5
allele num: 66310
num of homozygotes: 0

MQ
type: SiteQuality
SIO_000300: 5.937e1

QD
type: SiteQuality
SIO_000300: 1.047e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 5.22e-1

MQRankSum
type: SiteQuality
SIO_000300: 1.39e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.0e-4

DP
type: SiteQuality
SIO_000300: 1.501562e6

BaseQRankSum
type: SiteQuality
SIO_000300: 1.1e0

FS
type: SiteQuality
SIO_000300: 0.0e0

VQSLOD
type: SiteQuality
SIO_000300: 1.06e0

ClippingRankSum
type: SiteQuality
SIO_000300: 2.19e-1

GenotypeQuality
all individuals: 663
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 12
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 83
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 65
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 3802
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 128
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 6
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 82
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 44
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 93
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 2029
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 224
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 332
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 167
bin: 8.75e1
variant carriers: 0

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

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10328
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: 6580
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.508295625942685e-5
allele num: 66300
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8602
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16216
num of homozygotes: 0

InbreedingCoeff
type: SiteQuality
SIO_000300: -2.0e-4

ReadPosRankSum
type: SiteQuality
SIO_000300: 3.18e0

MQ
type: SiteQuality
SIO_000300: 5.953e1

ClippingRankSum
type: SiteQuality
SIO_000300: 5.75e-1

DP
type: SiteQuality
SIO_000300: 1.501921e6

BaseQRankSum
type: SiteQuality
SIO_000300: -4.45e-1

MQRankSum
type: SiteQuality
SIO_000300: 6.6e-2

FS
type: SiteQuality
SIO_000300: 1.694e0

QD
type: SiteQuality
SIO_000300: 9.18e0

VQSLOD
type: SiteQuality
SIO_000300: -1.073e0

GenotypeQuality
all individuals: 51559
bin: 6.25e1
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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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 (Non-Finnish)
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allele frequency: 0.0e0
allele num: 66310
num of homozygotes: 0

African
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allele frequency: 0.0e0
allele num: 10324
num of homozygotes: 0

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

East Asian
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allele count: 1
allele frequency: 1.163602513381429e-4
allele num: 8594
num of homozygotes: 0

Other
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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
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num of homozygotes: 0

South Asian
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ReadPosRankSum
type: SiteQuality
SIO_000300: -1.69e-1

MQ
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FS
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BaseQRankSum
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InbreedingCoeff
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SIO_000300: -1.0e-4

DP
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QD
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MQRankSum
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ClippingRankSum
type: SiteQuality
SIO_000300: 6.43e-1

VQSLOD
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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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 (Non-Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 66310
num of homozygotes: 0

Other
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allele frequency: 0.0e0
allele num: 896
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European (Finnish)
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allele count: 0
allele frequency: 0.0e0
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East Asian
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allele frequency: 1.163873370577281e-4
allele num: 8592
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

Latino
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allele frequency: 0.0e0
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African
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BaseQRankSum
type: SiteQuality
SIO_000300: -1.056e0

ClippingRankSum
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VQSLOD
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DP
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QD
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MQRankSum
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FS
type: SiteQuality
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InbreedingCoeff
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ReadPosRankSum
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MQ
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SIO_000300: 5.906e1

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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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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allele count: 0
allele frequency: 0.0e0
allele num: 6576
num of homozygotes: 0

East Asian
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allele frequency: 0.0e0
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Other
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allele frequency: 0.0e0
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South Asian
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allele count: 1
allele frequency: 6.175889328063241e-5
allele num: 16192
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Latino
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allele count: 0
allele frequency: 0.0e0
allele num: 11430
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African
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allele count: 0
allele frequency: 0.0e0
allele num: 10328
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European (Non-Finnish)
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allele count: 0
allele frequency: 0.0e0
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ClippingRankSum
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DP
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InbreedingCoeff
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BaseQRankSum
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VQSLOD
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ReadPosRankSum
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MQRankSum
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MQ
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FS
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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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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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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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num of homozygotes: 0

South Asian
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allele frequency: 0.0e0
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Latino
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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: 1.50879628232596e-5
allele num: 66278
num of homozygotes: 0

European (Finnish)
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allele count: 0
allele frequency: 0.0e0
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East Asian
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Other
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QD
type: SiteQuality
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BaseQRankSum
type: SiteQuality
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ReadPosRankSum
type: SiteQuality
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DP
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InbreedingCoeff
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VQSLOD
type: SiteQuality
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MQRankSum
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ClippingRankSum
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FS
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MQ
type: SiteQuality
SIO_000300: 5.951e1

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

European (Non-Finnish)
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allele count: 1
allele frequency: 1.512127260630255e-5
allele num: 66132
num of homozygotes: 0

European (Finnish)
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allele count: 0
allele frequency: 0.0e0
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African
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East Asian
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allele frequency: 0.0e0
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Latino
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allele frequency: 0.0e0
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South Asian
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DP
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ClippingRankSum
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BaseQRankSum
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QD
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VQSLOD
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InbreedingCoeff
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FS
type: SiteQuality
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MQRankSum
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MQ
type: SiteQuality
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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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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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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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num of homozygotes: 0

East Asian
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allele frequency: 0.0e0
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European (Finnish)
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allele frequency: 0.0e0
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African
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Latino
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European (Non-Finnish)
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allele count: 1
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allele num: 65108
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Other
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QD
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BaseQRankSum
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MQRankSum
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FS
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VQSLOD
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InbreedingCoeff
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DP
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ReadPosRankSum
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MQ
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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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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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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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Other
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Latino
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African
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East Asian
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South Asian
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European (Non-Finnish)
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allele num: 64932
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BaseQRankSum
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ReadPosRankSum
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FS
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DP
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MQ
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VQSLOD
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MQRankSum
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ClippingRankSum
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InbreedingCoeff
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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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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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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 (Non-Finnish)
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European (Finnish)
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Other
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African
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Latino
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East Asian
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South Asian
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MQRankSum
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ReadPosRankSum
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ClippingRankSum
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VQSLOD
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BaseQRankSum
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QD
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InbreedingCoeff
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FS
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DP
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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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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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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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Other
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European (Finnish)
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East Asian
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African
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European (Non-Finnish)
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South Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 15030
num of homozygotes: 0

BaseQRankSum
type: SiteQuality
SIO_000300: 3.37e-1

MQRankSum
type: SiteQuality
SIO_000300: -2.02e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.0e-3

QD
type: SiteQuality
SIO_000300: 1.774e1

ClippingRankSum
type: SiteQuality
SIO_000300: 1.19e0

DP
type: SiteQuality
SIO_000300: 1.391838e6

FS
type: SiteQuality
SIO_000300: 0.0e0

ReadPosRankSum
type: SiteQuality
SIO_000300: -1.416e0

VQSLOD
type: SiteQuality
SIO_000300: -2.866e0

MQ
type: SiteQuality
SIO_000300: 5.855e1

GenotypeQuality
all individuals: 462
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 360
bin: 5.25e1
variant carriers: 0

GenotypeQuality
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bin: 4.25e1
variant carriers: 0

GenotypeQuality
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bin: 7.5e0
variant carriers: 0

GenotypeQuality
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bin: 5.75e1
variant carriers: 0

GenotypeQuality
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bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1889
bin: 2.75e1
variant carriers: 0

GenotypeQuality
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bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 279
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2033
bin: 9.75e1
variant carriers: 4

GenotypeQuality
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bin: 2.25e1
variant carriers: 0

GenotypeQuality
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bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 158
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 443
bin: 7.75e1
variant carriers: 0

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

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10610
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6250
num of homozygotes: 0

East Asian
type: Population
allele count: 4
allele frequency: 5.045408678102926e-4
allele num: 7928
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 60250
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 14496
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9484
num of homozygotes: 0

ClippingRankSum
type: SiteQuality
SIO_000300: 3.81e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.6e-3

MQ
type: SiteQuality
SIO_000300: 6.0e1

QD
type: SiteQuality
SIO_000300: 1.261e1

BaseQRankSum
type: SiteQuality
SIO_000300: 2.15e0

FS
type: SiteQuality
SIO_000300: 3.771e0

DP
type: SiteQuality
SIO_000300: 1.326944e6

ReadPosRankSum
type: SiteQuality
SIO_000300: 3.7e-1

VQSLOD
type: SiteQuality
SIO_000300: 1.94e0

MQRankSum
type: SiteQuality
SIO_000300: 3.7e-1

GenotypeQuality
all individuals: 303
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 962
bin: 3.75e1
variant carriers: 0

GenotypeQuality
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bin: 7.5e0
variant carriers: 0

GenotypeQuality
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bin: 5.75e1
variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 220
bin: 9.25e1
variant carriers: 0

GenotypeQuality
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bin: 6.25e1
variant carriers: 0

GenotypeQuality
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bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 13602
bin: 2.25e1
variant carriers: 0

GenotypeQuality
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bin: 8.75e1
variant carriers: 0

GenotypeQuality
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bin: 7.25e1
variant carriers: 0

GenotypeQuality
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bin: 8.25e1
variant carriers: 0

GenotypeQuality
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bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 118
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 2029
bin: 9.75e1
variant carriers: 1

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9302
num of homozygotes: 0

South Asian
type: Population
allele count: 1
allele frequency: 7.054176072234762e-5
allele num: 14176
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10444
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 58996
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6168
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 816
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7762
num of homozygotes: 0

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.7e-3

QD
type: SiteQuality
SIO_000300: 1.007e1

BaseQRankSum
type: SiteQuality
SIO_000300: 2.76e0

VQSLOD
type: SiteQuality
SIO_000300: -4.811e-1

ClippingRankSum
type: SiteQuality
SIO_000300: 7.75e-1

FS
type: SiteQuality
SIO_000300: 1.871e0

MQRankSum
type: SiteQuality
SIO_000300: -1.023e0

ReadPosRankSum
type: SiteQuality
SIO_000300: -5.27e-1

DP
type: SiteQuality
SIO_000300: 1.284793e6

MQ
type: SiteQuality
SIO_000300: 5.919e1

GenotypeQuality
all individuals: 219
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2028
bin: 9.75e1
variant carriers: 0

GenotypeQuality
all individuals: 256
bin: 1.25e1
variant carriers: 0

GenotypeQuality
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bin: 2.5e0
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GenotypeQuality
all individuals: 1105
bin: 7.5e0
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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bin: 5.75e1
variant carriers: 0

GenotypeQuality
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bin: 8.75e1
variant carriers: 0

GenotypeQuality
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bin: 6.75e1
variant carriers: 0

GenotypeQuality
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bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 470
bin: 4.75e1
variant carriers: 1

GenotypeQuality
all individuals: 19001
bin: 6.25e1
variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6716
num of homozygotes: 0

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

South Asian
type: Population
allele count: 1
allele frequency: 7.844367743959836e-5
allele num: 12748
num of homozygotes: 0

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

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9360
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 52446
num of homozygotes: 0

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

VQSLOD
type: SiteQuality
SIO_000300: 2.51e0

MQ
type: SiteQuality
SIO_000300: 6.193e1

FS
type: SiteQuality
SIO_000300: 0.0e0

MQRankSum
type: SiteQuality
SIO_000300: -5.610000000000001e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -3.13e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.18e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 4.1e-3

BaseQRankSum
type: SiteQuality
SIO_000300: 1.83e0

DP
type: SiteQuality
SIO_000300: 1.082922e6

QD
type: SiteQuality
SIO_000300: 1.486e1

GenotypeQuality
all individuals: 628
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1432
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 16682
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2083
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1186
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variant carriers: 0

GenotypeQuality
all individuals: 4577
bin: 2.75e1
variant carriers: 0

GenotypeQuality
all individuals: 22653
bin: 2.25e1
variant carriers: 0

GenotypeQuality
all individuals: 265
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2034
bin: 9.75e1
variant carriers: 1

GenotypeQuality
all individuals: 461
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variant carriers: 0

GenotypeQuality
all individuals: 217
bin: 9.25e1
variant carriers: 0

GenotypeQuality
all individuals: 153
bin: 8.75e1
variant carriers: 0

South Asian
type: Population
allele count: 1
allele frequency: 8.19000819000819e-5
allele num: 12210
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5748
num of homozygotes: 0

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

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.981296560469171e-5
allele num: 50472
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9066
num of homozygotes: 0

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

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6458
num of homozygotes: 0

MQRankSum
type: SiteQuality
SIO_000300: 4.58e-1

VQSLOD
type: SiteQuality
SIO_000300: 2.3e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.49e-2

BaseQRankSum
type: SiteQuality
SIO_000300: -8.39e-1

QD
type: SiteQuality
SIO_000300: 6.46e0

FS
type: SiteQuality
SIO_000300: 1.136e0

MQ
type: SiteQuality
SIO_000300: 6.026e1

ClippingRankSum
type: SiteQuality
SIO_000300: 0.0e0

ReadPosRankSum
type: SiteQuality
SIO_000300: -2.77e-1

DP
type: SiteQuality
SIO_000300: 1.066886e6

GenotypeQuality
all individuals: 597
bin: 1.25e1
variant carriers: 0

GenotypeQuality
all individuals: 4577
bin: 2.75e1
variant carriers: 2

GenotypeQuality
all individuals: 2083
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 355
bin: 7.75e1
variant carriers: 3

GenotypeQuality
all individuals: 577
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1432
bin: 7.5e0
variant carriers: 1

GenotypeQuality
all individuals: 461
bin: 5.75e1
variant carriers: 1

GenotypeQuality
all individuals: 596
bin: 5.25e1
variant carriers: 1

GenotypeQuality
all individuals: 4672
bin: 3.25e1
variant carriers: 1

GenotypeQuality
all individuals: 313
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variant carriers: 1

GenotypeQuality
all individuals: 16682
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 217
bin: 9.25e1
variant carriers: 2

Latino
type: Population
allele count: 5
allele frequency: 5.515111405250386e-4
allele num: 9066
num of homozygotes: 0

African
type: Population
allele count: 27
allele frequency: 3.31207065750736e-3
allele num: 8152
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6458
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 3
allele frequency: 5.943889681407513e-5
allele num: 50472
num of homozygotes: 0

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

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5748
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 12210
num of homozygotes: 0

QD
type: SiteQuality
SIO_000300: 6.46e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.49e-2

DP
type: SiteQuality
SIO_000300: 1.066886e6

FS
type: SiteQuality
SIO_000300: 1.136e0

ClippingRankSum
type: SiteQuality
SIO_000300: 0.0e0

BaseQRankSum
type: SiteQuality
SIO_000300: -8.39e-1

MQ
type: SiteQuality
SIO_000300: 6.026e1

ReadPosRankSum
type: SiteQuality
SIO_000300: -2.77e-1

VQSLOD
type: SiteQuality
SIO_000300: 2.3e0

MQRankSum
type: SiteQuality
SIO_000300: 4.58e-1

GenotypeQuality
all individuals: 461
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 16682
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 597
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variant carriers: 0

GenotypeQuality
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bin: 2.25e1
variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 4577
bin: 2.75e1
variant carriers: 1

GenotypeQuality
all individuals: 2034
bin: 9.75e1
variant carriers: 1

GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 628
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 596
bin: 5.25e1
variant carriers: 0

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

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 12210
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6458
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 2
allele frequency: 3.962593120938342e-5
allele num: 50472
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5748
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9066
num of homozygotes: 0

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

ReadPosRankSum
type: SiteQuality
SIO_000300: -2.77e-1

FS
type: SiteQuality
SIO_000300: 1.136e0

DP
type: SiteQuality
SIO_000300: 1.066886e6

VQSLOD
type: SiteQuality
SIO_000300: 2.3e0

ClippingRankSum
type: SiteQuality
SIO_000300: 0.0e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.49e-2

MQRankSum
type: SiteQuality
SIO_000300: 4.58e-1

MQ
type: SiteQuality
SIO_000300: 6.026e1

QD
type: SiteQuality
SIO_000300: 6.46e0

BaseQRankSum
type: SiteQuality
SIO_000300: -8.39e-1

GenotypeQuality
all individuals: 80
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 5984
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 2667
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variant carriers: 0

GenotypeQuality
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variant carriers: 1

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
all individuals: 598
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 216
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GenotypeQuality
all individuals: 269
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GenotypeQuality
all individuals: 2020
bin: 9.75e1
variant carriers: 3

GenotypeQuality
all individuals: 12421
bin: 6.25e1
variant carriers: 0

African
type: Population
allele count: 4
allele frequency: 4.972650422675286e-4
allele num: 8044
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8872
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 49476
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 704
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5666
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 12106
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6194
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 0.0e0

QD
type: SiteQuality
SIO_000300: 1.002e1

ReadPosRankSum
type: SiteQuality
SIO_000300: -3.95e-1

MQRankSum
type: SiteQuality
SIO_000300: 2.96e-1

DP
type: SiteQuality
SIO_000300: 9.80877e5

ClippingRankSum
type: SiteQuality
SIO_000300: 3.06e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 9.21e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -4.9e-3

VQSLOD
type: SiteQuality
SIO_000300: 4.36e-1

GenotypeQuality
all individuals: 3059
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 832
bin: 1.75e1
variant carriers: 0

GenotypeQuality
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variant carriers: 1

GenotypeQuality
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GenotypeQuality
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bin: 2.75e1
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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: 5.25e1
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GenotypeQuality
all individuals: 349
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variant carriers: 0

GenotypeQuality
all individuals: 290
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GenotypeQuality
all individuals: 496
bin: 4.75e1
variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6040
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7862
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 2.070393374741201e-5
allele num: 48300
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8670
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 694
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11838
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5600
num of homozygotes: 0

MQ
type: SiteQuality
SIO_000300: 5.911e1

MQRankSum
type: SiteQuality
SIO_000300: -1.051e0

VQSLOD
type: SiteQuality
SIO_000300: -1.697e0

FS
type: SiteQuality
SIO_000300: 7.327e0

ClippingRankSum
type: SiteQuality
SIO_000300: -1.03e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: -6.0e-3

ReadPosRankSum
type: SiteQuality
SIO_000300: 5.37e-1

DP
type: SiteQuality
SIO_000300: 9.50369e5

BaseQRankSum
type: SiteQuality
SIO_000300: -5.37e-1

QD
type: SiteQuality
SIO_000300: 8.17e0

GenotypeQuality
all individuals: 4363
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 83
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
all individuals: 1546
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GenotypeQuality
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GenotypeQuality
all individuals: 6405
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GenotypeQuality
all individuals: 1804
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variant carriers: 0

GenotypeQuality
all individuals: 1165
bin: 4.25e1
variant carriers: 0

GenotypeQuality
all individuals: 152
bin: 8.75e1
variant carriers: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5278
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7892
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 5410
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 2.321047256522143e-5
allele num: 43084
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 650
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 7010
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10724
num of homozygotes: 0

ClippingRankSum
type: SiteQuality
SIO_000300: 9.56e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

MQRankSum
type: SiteQuality
SIO_000300: -9.9e-2

ReadPosRankSum
type: SiteQuality
SIO_000300: -9.56e-1

QD
type: SiteQuality
SIO_000300: 1.23e1

VQSLOD
type: SiteQuality
SIO_000300: 3.16e-1

FS
type: SiteQuality
SIO_000300: 0.0e0

InbreedingCoeff
type: SiteQuality
SIO_000300: -8.699999999999999e-3

BaseQRankSum
type: SiteQuality
SIO_000300: 3.79e0

DP
type: SiteQuality
SIO_000300: 8.51181e5

GenotypeQuality
all individuals: 186
bin: 5.75e1
variant carriers: 0

GenotypeQuality
all individuals: 6946
bin: 1.75e1
variant carriers: 0

GenotypeQuality
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bin: 7.5e0
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GenotypeQuality
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bin: 3.75e1
variant carriers: 0

GenotypeQuality
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bin: 9.75e1
variant carriers: 1

GenotypeQuality
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bin: 6.75e1
variant carriers: 0

GenotypeQuality
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bin: 4.25e1
variant carriers: 0

GenotypeQuality
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bin: 8.75e1
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GenotypeQuality
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bin: 7.75e1
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GenotypeQuality
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bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 1818
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 15771
bin: 2.25e1
variant carriers: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9486
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6982
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 4850
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 2.669799231097821e-5
allele num: 37456
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 4602
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 588
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6172
num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: -2.832e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 2.31e-1

FS
type: SiteQuality
SIO_000300: 0.0e0

MQRankSum
type: SiteQuality
SIO_000300: -2.31e-1

QD
type: SiteQuality
SIO_000300: 2.37e0

DP
type: SiteQuality
SIO_000300: 8.02843e5

BaseQRankSum
type: SiteQuality
SIO_000300: 2.31e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -2.31e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

InbreedingCoeff
type: SiteQuality
SIO_000300: -1.15e-2

GenotypeQuality
all individuals: 918
bin: 3.25e1
variant carriers: 0

GenotypeQuality
all individuals: 7903
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 1

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 1608
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variant carriers: 0

GenotypeQuality
all individuals: 558
bin: 2.75e1
variant carriers: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 15928
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 65502
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 884
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6594
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8522
num of homozygotes: 0

African
type: Population
allele count: 1
allele frequency: 9.942334460131238e-5
allele num: 10058
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11472
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 3.078e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.61e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.06e-2

MQ
type: SiteQuality
SIO_000300: 6.033e1

ClippingRankSum
type: SiteQuality
SIO_000300: -3.48e-1

VQSLOD
type: SiteQuality
SIO_000300: 1.52e0

BaseQRankSum
type: SiteQuality
SIO_000300: 2.12e0

QD
type: SiteQuality
SIO_000300: 1.595e1

MQRankSum
type: SiteQuality
SIO_000300: -2.43e-1

DP
type: SiteQuality
SIO_000300: 1.639054e6

GenotypeQuality
all individuals: 451
bin: 3.75e1
variant carriers: 0

GenotypeQuality
all individuals: 403
bin: 9.25e1
variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 70
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variant carriers: 0

GenotypeQuality
all individuals: 1893
bin: 9.75e1
variant carriers: 2

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16110
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10162
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 890
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 2
allele frequency: 3.04062271953296e-5
allele num: 65776
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11500
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6594
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8580
num of homozygotes: 0

ReadPosRankSum
type: SiteQuality
SIO_000300: 7.41e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 4.66e0

DP
type: SiteQuality
SIO_000300: 1.660561e6

FS
type: SiteQuality
SIO_000300: 0.0e0

MQRankSum
type: SiteQuality
SIO_000300: 3.65e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -7.02e-1

MQ
type: SiteQuality
SIO_000300: 5.966e1

VQSLOD
type: SiteQuality
SIO_000300: 4.95e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 6.9e-3

QD
type: SiteQuality
SIO_000300: 1.611e1

GenotypeQuality
all individuals: 8
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 80
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variant carriers: 0

GenotypeQuality
all individuals: 18
bin: 2.5e0
variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 1

GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 89
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variant carriers: 0

GenotypeQuality
all individuals: 112
bin: 5.25e1
variant carriers: 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: 11538
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10250
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8614
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16316
num of homozygotes: 0

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

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.512172992590352e-5
allele num: 66130
num of homozygotes: 0

FS
type: SiteQuality
SIO_000300: 1.289e0

MQRankSum
type: SiteQuality
SIO_000300: 6.55e-1

BaseQRankSum
type: SiteQuality
SIO_000300: 3.03e0

ClippingRankSum
type: SiteQuality
SIO_000300: -1.131e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.14e0

MQ
type: SiteQuality
SIO_000300: 5.915e1

VQSLOD
type: SiteQuality
SIO_000300: 6.31e-1

DP
type: SiteQuality
SIO_000300: 1.676524e6

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.18e-2

QD
type: SiteQuality
SIO_000300: 1.246e1

GenotypeQuality
all individuals: 12
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 44777
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 8177
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 377
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GenotypeQuality
all individuals: 1885
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variant carriers: 1

GenotypeQuality
all individuals: 848
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
all individuals: 1657
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variant carriers: 0

GenotypeQuality
all individuals: 1625
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 405
bin: 9.25e1
variant carriers: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66318
num of homozygotes: 0

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

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10306
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8622
num of homozygotes: 0

Latino
type: Population
allele count: 1
allele frequency: 8.652015919709292e-5
allele num: 11558
num of homozygotes: 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: 16386
num of homozygotes: 0

QD
type: SiteQuality
SIO_000300: 1.017e1

MQ
type: SiteQuality
SIO_000300: 5.947e1

VQSLOD
type: SiteQuality
SIO_000300: 3.93e-1

MQRankSum
type: SiteQuality
SIO_000300: 1.27e0

DP
type: SiteQuality
SIO_000300: 1.682428e6

FS
type: SiteQuality
SIO_000300: 1.22e0

BaseQRankSum
type: SiteQuality
SIO_000300: -3.467e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.01e-2

ClippingRankSum
type: SiteQuality
SIO_000300: 4.8e-2

ReadPosRankSum
type: SiteQuality
SIO_000300: 6.97e-1

GenotypeQuality
all individuals: 850
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 98
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variant carriers: 0

GenotypeQuality
all individuals: 44993
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 47
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GenotypeQuality
all individuals: 1887
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variant carriers: 3

GenotypeQuality
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GenotypeQuality
all individuals: 32
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
all individuals: 11
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variant carriers: 0

GenotypeQuality
all individuals: 3
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variant carriers: 0

GenotypeQuality
all individuals: 331
bin: 8.75e1
variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8624
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10340
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: 11554
num of homozygotes: 0

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

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

European (Non-Finnish)
type: Population
allele count: 3
allele frequency: 4.518072289156627e-5
allele num: 66400
num of homozygotes: 0

MQRankSum
type: SiteQuality
SIO_000300: -4.69e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 5.99e-1

MQ
type: SiteQuality
SIO_000300: 5.981e1

FS
type: SiteQuality
SIO_000300: 1.897e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 6.1e-3

DP
type: SiteQuality
SIO_000300: 1.685383e6

VQSLOD
type: SiteQuality
SIO_000300: 8.93e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -4.31e0

ClippingRankSum
type: SiteQuality
SIO_000300: -8.169999999999999e-1

QD
type: SiteQuality
SIO_000300: 1.515e1

GenotypeQuality
all individuals: 1897
bin: 9.75e1
variant carriers: 30

GenotypeQuality
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variant carriers: 0

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

GenotypeQuality
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bin: 7.25e1
variant carriers: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16436
num of homozygotes: 0

African
type: Population
allele count: 29
allele frequency: 2.801932367149759e-3
allele num: 10350
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66448
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: 1
allele frequency: 8.650519031141868e-5
allele num: 11560
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8632
num of homozygotes: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 902
num of homozygotes: 0

InbreedingCoeff
type: SiteQuality
SIO_000300: 4.6e-3

FS
type: SiteQuality
SIO_000300: 0.0e0

DP
type: SiteQuality
SIO_000300: 1.687525e6

QD
type: SiteQuality
SIO_000300: 1.321e1

ClippingRankSum
type: SiteQuality
SIO_000300: -5.52e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -2.051e0

MQRankSum
type: SiteQuality
SIO_000300: 1.27e-1

VQSLOD
type: SiteQuality
SIO_000300: 6.32e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 4.28e-1

MQ
type: SiteQuality
SIO_000300: 5.967e1

GenotypeQuality
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bin: 3.25e1
variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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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: 9.25e1
variant carriers: 0

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

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10372
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.502042778178322e-5
allele num: 66576
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 16480
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11568
num of homozygotes: 0

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

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

MQ
type: SiteQuality
SIO_000300: 5.966e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 3.0e-3

DP
type: SiteQuality
SIO_000300: 1.689136e6

ClippingRankSum
type: SiteQuality
SIO_000300: -3.14e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 2.5e-3

FS
type: SiteQuality
SIO_000300: 6.071e0

MQRankSum
type: SiteQuality
SIO_000300: 1.31e0

BaseQRankSum
type: SiteQuality
SIO_000300: 3.01e0

VQSLOD
type: SiteQuality
SIO_000300: -6.924e-1

QD
type: SiteQuality
SIO_000300: 1.761e1

GenotypeQuality
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variant carriers: 0

GenotypeQuality
all individuals: 1660
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
all individuals: 21
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GenotypeQuality
all individuals: 330
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
all individuals: 30
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variant carriers: 0

GenotypeQuality
all individuals: 404
bin: 9.25e1
variant carriers: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66594
num of homozygotes: 0

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

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

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

South Asian
type: Population
allele count: 1
allele frequency: 6.065752759917505e-5
allele num: 16486
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11568
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8640
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BaseQRankSum
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SIO_000300: -4.545e0

MQ
type: SiteQuality
SIO_000300: 5.955e1

VQSLOD
type: SiteQuality
SIO_000300: 7.41e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.11e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 2.0e-3

DP
type: SiteQuality
SIO_000300: 1.689654e6

FS
type: SiteQuality
SIO_000300: 4.652e0

QD
type: SiteQuality
SIO_000300: 1.446e1

ClippingRankSum
type: SiteQuality
SIO_000300: -1.86e0

MQRankSum
type: SiteQuality
SIO_000300: -4.63e-1

GenotypeQuality
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bin: 1.25e1
variant carriers: 0

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

GenotypeQuality
all individuals: 405
bin: 9.25e1
variant carriers: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8640
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.500555205426008e-5
allele num: 66642
num of homozygotes: 0

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

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11568
num of homozygotes: 0

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

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

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

FS
type: SiteQuality
SIO_000300: 3.568e0

MQ
type: SiteQuality
SIO_000300: 5.938e1

MQRankSum
type: SiteQuality
SIO_000300: 2.8e-1

QD
type: SiteQuality
SIO_000300: 1.335e1

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.0e-4

ClippingRankSum
type: SiteQuality
SIO_000300: -1.076e0

VQSLOD
type: SiteQuality
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DP
type: SiteQuality
SIO_000300: 1.690594e6

BaseQRankSum
type: SiteQuality
SIO_000300: 2.93e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 8.89e-1

GenotypeQuality
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variant carriers: 0

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

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11568
num of homozygotes: 0

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

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

African
type: Population
allele count: 1
allele frequency: 9.624639076034648e-5
allele num: 10390
num of homozygotes: 0

South Asian
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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: 6612
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66646
num of homozygotes: 0

InbreedingCoeff
type: SiteQuality
SIO_000300: 8.0e-4

ClippingRankSum
type: SiteQuality
SIO_000300: -1.1e-2

DP
type: SiteQuality
SIO_000300: 1.691204e6

MQRankSum
type: SiteQuality
SIO_000300: 6.870000000000001e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -3.271e0

QD
type: SiteQuality
SIO_000300: 1.377e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 2.4e-2

FS
type: SiteQuality
SIO_000300: 1.065e0

VQSLOD
type: SiteQuality
SIO_000300: 8.19e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

GenotypeQuality
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variant carriers: 0

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

East Asian
type: Population
allele count: 1
allele frequency: 1.157139551029854e-4
allele num: 8642
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66670
num of homozygotes: 0

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

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 10394
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11568
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6612
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: -2.0e-2

VQSLOD
type: SiteQuality
SIO_000300: 2.07e0

MQ
type: SiteQuality
SIO_000300: 5.925e1

FS
type: SiteQuality
SIO_000300: 0.0e0

DP
type: SiteQuality
SIO_000300: 1.691516e6

QD
type: SiteQuality
SIO_000300: 1.34e1

BaseQRankSum
type: SiteQuality
SIO_000300: 3.93e0

ClippingRankSum
type: SiteQuality
SIO_000300: -1.403e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 2.96e-1

GenotypeQuality
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variant carriers: 0

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

East Asian
type: Population
allele count: 6
allele frequency: 6.942837306179125e-4
allele num: 8642
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 13
allele frequency: 1.949668556345421e-4
allele num: 66678
num of homozygotes: 0

Latino
type: Population
allele count: 2
allele frequency: 1.728907330567082e-4
allele num: 11568
num of homozygotes: 0

African
type: Population
allele count: 2
allele frequency: 1.923816852635629e-4
allele num: 10396
num of homozygotes: 0

South Asian
type: Population
allele count: 9
allele frequency: 5.453223460979156e-4
allele num: 16504
num of homozygotes: 1

Other
type: Population
allele count: 1
allele frequency: 1.101321585903084e-3
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

BaseQRankSum
type: SiteQuality
SIO_000300: 3.5e0

QD
type: SiteQuality
SIO_000300: 1.414e1

FS
type: SiteQuality
SIO_000300: 0.0e0

VQSLOD
type: SiteQuality
SIO_000300: 5.18e0

InbreedingCoeff
type: SiteQuality
SIO_000300: 1.81e-2

MQRankSum
type: SiteQuality
SIO_000300: 2.83e-1

ClippingRankSum
type: SiteQuality
SIO_000300: -3.98e-1

DP
type: SiteQuality
SIO_000300: 1.694193e6

MQ
type: SiteQuality
SIO_000300: 5.963e1

ReadPosRankSum
type: SiteQuality
SIO_000300: 3.99e-1

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
all individuals: 8280
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variant carriers: 0

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

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

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

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 66688
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
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South Asian
type: Population
allele count: 2
allele frequency: 1.211680600993578e-4
allele num: 16506
num of homozygotes: 0

VQSLOD
type: SiteQuality
SIO_000300: -2.792e0

MQRankSum
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FS
type: SiteQuality
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InbreedingCoeff
type: SiteQuality
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QD
type: SiteQuality
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ClippingRankSum
type: SiteQuality
SIO_000300: 1.67e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -5.54e-1

ReadPosRankSum
type: SiteQuality
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DP
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SIO_000300: 1.692155e6

MQ
type: SiteQuality
SIO_000300: 5.98e1

GenotypeQuality
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variant carriers: 0

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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bin: 6.75e1
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Latino
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allele count: 0
allele frequency: 0.0e0
allele num: 11572
num of homozygotes: 0

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

European (Non-Finnish)
type: Population
allele count: 4
allele frequency: 5.995203836930456e-5
allele num: 66720
num of homozygotes: 0

South 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

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

African
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allele count: 0
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allele num: 10404
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ClippingRankSum
type: SiteQuality
SIO_000300: 2.6e-1

InbreedingCoeff
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BaseQRankSum
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ReadPosRankSum
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MQ
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MQRankSum
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DP
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QD
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FS
type: SiteQuality
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VQSLOD
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GenotypeQuality
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variant carriers: 3

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

European (Finnish)
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allele count: 0
allele frequency: 0.0e0
allele num: 6612
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)
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allele count: 3
allele frequency: 4.497211728728189e-5
allele num: 66708
num of homozygotes: 0

Latino
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allele frequency: 0.0e0
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num of homozygotes: 0

African
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allele frequency: 0.0e0
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East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8646
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: 1.693229e6

BaseQRankSum
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VQSLOD
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MQ
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MQRankSum
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FS
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QD
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ClippingRankSum
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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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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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: 0
allele frequency: 0.0e0
allele num: 16506
num of homozygotes: 0

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

East Asian
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allele count: 0
allele frequency: 0.0e0
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European (Non-Finnish)
type: Population
allele count: 1
allele frequency: 1.49907057624273e-5
allele num: 66708
num of homozygotes: 0

African
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Latino
type: Population
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num of homozygotes: 0

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

GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
all individuals: 4
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GenotypeQuality
all individuals: 7
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variant carriers: 0

Other
type: Population
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African
type: Population
allele count: 1
allele frequency: 9.609840476648087e-5
allele num: 10406
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11570
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
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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 frequency: 0.0e0
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InbreedingCoeff
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ClippingRankSum
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VQSLOD
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MQ
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DP
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BaseQRankSum
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QD
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MQRankSum
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ReadPosRankSum
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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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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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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: 66728
num of homozygotes: 0

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

Latino
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allele frequency: 0.0e0
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num of homozygotes: 0

African
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allele frequency: 0.0e0
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Other
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East Asian
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allele frequency: 0.0e0
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South Asian
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allele num: 16510
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FS
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VQSLOD
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QD
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MQRankSum
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MQ
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ClippingRankSum
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BaseQRankSum
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InbreedingCoeff
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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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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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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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num of homozygotes: 0

African
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allele frequency: 0.0e0
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European (Non-Finnish)
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allele frequency: 7.49265719594797e-5
allele num: 66732
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European (Finnish)
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allele frequency: 0.0e0
allele num: 6612
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Latino
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East Asian
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allele frequency: 0.0e0
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South Asian
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allele frequency: 0.0e0
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VQSLOD
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MQRankSum
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QD
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FS
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InbreedingCoeff
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ClippingRankSum
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BaseQRankSum
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ReadPosRankSum
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MQ
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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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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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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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African
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allele num: 10406
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European (Finnish)
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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: 1.348678295270635e-4
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Other
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East Asian
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Latino
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allele frequency: 3.456022118541559e-4
allele num: 11574
num of homozygotes: 0

FS
type: SiteQuality
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InbreedingCoeff
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DP
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MQRankSum
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VQSLOD
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ReadPosRankSum
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MQ
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QD
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ClippingRankSum
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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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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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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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Other
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African
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allele frequency: 0.0e0
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European (Non-Finnish)
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allele frequency: 1.498621268433042e-5
allele num: 66728
num of homozygotes: 0

Latino
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allele frequency: 0.0e0
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num of homozygotes: 0

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

South Asian
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MQRankSum
type: SiteQuality
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BaseQRankSum
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MQ
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ReadPosRankSum
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DP
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QD
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InbreedingCoeff
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VQSLOD
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FS
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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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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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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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Other
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East Asian
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African
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South Asian
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European (Non-Finnish)
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allele num: 66732
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Latino
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MQRankSum
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FS
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ReadPosRankSum
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BaseQRankSum
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InbreedingCoeff
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DP
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ClippingRankSum
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VQSLOD
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MQ
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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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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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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 (Non-Finnish)
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num of homozygotes: 0

European (Finnish)
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Other
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Latino
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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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VQSLOD
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MQ
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QD
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InbreedingCoeff
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MQRankSum
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DP
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ClippingRankSum
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BaseQRankSum
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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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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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African
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East Asian
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Other
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European (Non-Finnish)
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South Asian
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Latino
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European (Finnish)
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InbreedingCoeff
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ClippingRankSum
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DP
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FS
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BaseQRankSum
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QD
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MQRankSum
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MQ
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ReadPosRankSum
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VQSLOD
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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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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European (Non-Finnish)
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Other
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Latino
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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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ReadPosRankSum
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QD
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FS
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ClippingRankSum
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MQ
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VQSLOD
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DP
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InbreedingCoeff
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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African
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European (Non-Finnish)
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East Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 8652
num of homozygotes: 0

Latino
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allele count: 0
allele frequency: 0.0e0
allele num: 11568
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South Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 16512
num of homozygotes: 0

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

BaseQRankSum
type: SiteQuality
SIO_000300: -6.377e0

FS
type: SiteQuality
SIO_000300: 4.28e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 1.19e0

VQSLOD
type: SiteQuality
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QD
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SIO_000300: 1.461e1

ClippingRankSum
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SIO_000300: -7.66e-1

MQRankSum
type: SiteQuality
SIO_000300: 3.75e-1

InbreedingCoeff
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SIO_000300: -1.0e-4

DP
type: SiteQuality
SIO_000300: 1.693268e6

MQ
type: SiteQuality
SIO_000300: 5.954e1

GenotypeQuality
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variant carriers: 0

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

African
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allele count: 0
allele frequency: 0.0e0
allele num: 10406
num of homozygotes: 0

South Asian
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allele frequency: 0.0e0
allele num: 16512
num of homozygotes: 0

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

European (Non-Finnish)
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allele count: 2
allele frequency: 2.997152704930316e-5
allele num: 66730
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

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

DP
type: SiteQuality
SIO_000300: 1.693333e6

ReadPosRankSum
type: SiteQuality
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VQSLOD
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ClippingRankSum
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InbreedingCoeff
type: SiteQuality
SIO_000300: -2.0e-4

FS
type: SiteQuality
SIO_000300: 5.3e-1

MQ
type: SiteQuality
SIO_000300: 5.966e1

MQRankSum
type: SiteQuality
SIO_000300: 8.86e-1

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

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

Other
type: Population
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
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Latino
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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: 66730
num of homozygotes: 0

East Asian
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allele frequency: 0.0e0
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South Asian
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allele num: 16512
num of homozygotes: 0

InbreedingCoeff
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QD
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ClippingRankSum
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MQ
type: SiteQuality
SIO_000300: 6.0e1

ReadPosRankSum
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MQRankSum
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SIO_000300: -3.47e-1

VQSLOD
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FS
type: SiteQuality
SIO_000300: 6.879999999999999e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -4.423e0

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

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

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

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

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

East Asian
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allele count: 1
allele frequency: 1.155802126675913e-4
allele num: 8652
num of homozygotes: 0

South Asian
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allele count: 0
allele frequency: 0.0e0
allele num: 16512
num of homozygotes: 0

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

InbreedingCoeff
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DP
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FS
type: SiteQuality
SIO_000300: 6.32e-1

BaseQRankSum
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MQRankSum
type: SiteQuality
SIO_000300: -1.968e0

ClippingRankSum
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SIO_000300: 3.06e0

VQSLOD
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MQ
type: SiteQuality
SIO_000300: 5.983e1

QD
type: SiteQuality
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ReadPosRankSum
type: SiteQuality
SIO_000300: -3.041e0

GenotypeQuality
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variant carriers: 0

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

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

African
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allele count: 0
allele frequency: 0.0e0
allele num: 10406
num of homozygotes: 0

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

South Asian
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allele count: 1
allele frequency: 6.056201550387597e-5
allele num: 16512
num of homozygotes: 0

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

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

BaseQRankSum
type: SiteQuality
SIO_000300: -4.332e0

DP
type: SiteQuality
SIO_000300: 1.693016e6

VQSLOD
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SIO_000300: -1.301e0

ClippingRankSum
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SIO_000300: 1.07e0

FS
type: SiteQuality
SIO_000300: 0.0e0

InbreedingCoeff
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MQ
type: SiteQuality
SIO_000300: 5.875e1

QD
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MQRankSum
type: SiteQuality
SIO_000300: -7.8e-1

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

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

African
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allele count: 0
allele frequency: 0.0e0
allele num: 10406
num of homozygotes: 0

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

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

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

South Asian
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allele frequency: 1.211240310077519e-4
allele num: 16512
num of homozygotes: 0

DP
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BaseQRankSum
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ClippingRankSum
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MQ
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InbreedingCoeff
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FS
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MQRankSum
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VQSLOD
type: SiteQuality
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ReadPosRankSum
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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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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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 frequency: 3.028100775193798e-4
allele num: 16512
num of homozygotes: 0

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

African
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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
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num of homozygotes: 0

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

FS
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ReadPosRankSum
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InbreedingCoeff
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BaseQRankSum
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MQ
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ClippingRankSum
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QD
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VQSLOD
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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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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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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
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num of homozygotes: 0

European (Finnish)
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allele frequency: 0.0e0
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East Asian
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allele frequency: 0.0e0
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European (Non-Finnish)
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allele num: 66726
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African
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South Asian
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Latino
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num of homozygotes: 0

FS
type: SiteQuality
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ClippingRankSum
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MQ
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InbreedingCoeff
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VQSLOD
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MQRankSum
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BaseQRankSum
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QD
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ReadPosRankSum
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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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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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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 (Non-Finnish)
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allele count: 0
allele frequency: 0.0e0
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East Asian
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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
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South Asian
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allele count: 1
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allele num: 16512
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Latino
type: Population
allele count: 0
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Other
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QD
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VQSLOD
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MQRankSum
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ReadPosRankSum
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FS
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BaseQRankSum
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MQ
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DP
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InbreedingCoeff
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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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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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variant carriers: 0

European (Non-Finnish)
type: Population
allele count: 15
allele frequency: 2.248134048739546e-4
allele num: 66722
num of homozygotes: 0

East Asian
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African
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Latino
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Other
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European (Finnish)
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South Asian
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InbreedingCoeff
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DP
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BaseQRankSum
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ReadPosRankSum
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MQ
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ClippingRankSum
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VQSLOD
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MQRankSum
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FS
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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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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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African
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European (Non-Finnish)
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South Asian
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Other
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East Asian
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European (Finnish)
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VQSLOD
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ClippingRankSum
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DP
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InbreedingCoeff
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MQ
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BaseQRankSum
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QD
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MQRankSum
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FS
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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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GenotypeQuality
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GenotypeQuality
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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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European (Finnish)
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East Asian
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Latino
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African
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European (Non-Finnish)
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Other
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VQSLOD
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MQRankSum
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DP
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ReadPosRankSum
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QD
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BaseQRankSum
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MQ
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FS
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ClippingRankSum
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InbreedingCoeff
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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European (Non-Finnish)
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African
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East Asian
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Other
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European (Finnish)
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Latino
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South Asian
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InbreedingCoeff
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MQRankSum
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VQSLOD
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MQ
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FS
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BaseQRankSum
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ClippingRankSum
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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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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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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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Latino
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South Asian
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African
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Other
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European (Non-Finnish)
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European (Finnish)
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VQSLOD
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MQRankSum
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MQ
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QD
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InbreedingCoeff
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FS
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DP
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ReadPosRankSum
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BaseQRankSum
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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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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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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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Latino
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East Asian
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European (Non-Finnish)
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Other
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African
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South Asian
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ReadPosRankSum
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MQRankSum
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DP
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MQ
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VQSLOD
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InbreedingCoeff
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ClippingRankSum
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FS
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QD
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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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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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African
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European (Non-Finnish)
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Latino
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Other
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South Asian
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East Asian
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European (Finnish)
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MQ
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BaseQRankSum
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VQSLOD
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QD
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ReadPosRankSum
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MQRankSum
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InbreedingCoeff
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FS
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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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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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African
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European (Non-Finnish)
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European (Finnish)
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Latino
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East Asian
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MQ
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ReadPosRankSum
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QD
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FS
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VQSLOD
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DP
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MQRankSum
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InbreedingCoeff
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BaseQRankSum
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ClippingRankSum
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GenotypeQuality
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European (Non-Finnish)
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African
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European (Finnish)
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East Asian
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South Asian
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Latino
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ReadPosRankSum
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ClippingRankSum
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BaseQRankSum
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InbreedingCoeff
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FS
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MQRankSum
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DP
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QD
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MQ
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GenotypeQuality
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GenotypeQuality
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GenotypeQuality
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bin: 8.25e1
variant carriers: 0

South Asian
type: Population
allele count: 1
allele frequency: 6.201165819174004e-5
allele num: 16126
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 65950
num of homozygotes: 0

East Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 8478
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6576
num of homozygotes: 0

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11460
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9944
num of homozygotes: 0

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

VQSLOD
type: SiteQuality
SIO_000300: -1.117e0

ReadPosRankSum
type: SiteQuality
SIO_000300: 8.51e-1

BaseQRankSum
type: SiteQuality
SIO_000300: -2.466e0

FS
type: SiteQuality
SIO_000300: 6.229e0

MQ
type: SiteQuality
SIO_000300: 5.878e1

MQRankSum
type: SiteQuality
SIO_000300: -5.87e-1

InbreedingCoeff
type: SiteQuality
SIO_000300: 8.0e-4

DP
type: SiteQuality
SIO_000300: 1.660593e6

QD
type: SiteQuality
SIO_000300: 1.222e1

ClippingRankSum
type: SiteQuality
SIO_000300: -7.34e-1

GenotypeQuality
all individuals: 27
bin: 1.75e1
variant carriers: 0

GenotypeQuality
all individuals: 42626
bin: 6.25e1
variant carriers: 0

GenotypeQuality
all individuals: 17
bin: 2.5e0
variant carriers: 0

GenotypeQuality
all individuals: 97
bin: 4.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1811
bin: 9.75e1
variant carriers: 10

GenotypeQuality
all individuals: 317
bin: 8.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1559
bin: 7.25e1
variant carriers: 0

GenotypeQuality
all individuals: 797
bin: 8.25e1
variant carriers: 0

GenotypeQuality
all individuals: 172
bin: 5.25e1
variant carriers: 0

GenotypeQuality
all individuals: 7871
bin: 6.75e1
variant carriers: 0

GenotypeQuality
all individuals: 1539
bin: 7.75e1
variant carriers: 0

GenotypeQuality
all individuals: 144
bin: 7.5e0
variant carriers: 0

GenotypeQuality
all individuals: 389
bin: 9.25e1
variant carriers: 0

Other
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 888
num of homozygotes: 0

European (Non-Finnish)
type: Population
allele count: 10
allele frequency: 1.523600572873815e-4
allele num: 65634
num of homozygotes: 0

European (Finnish)
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 6566
num of homozygotes: 0

South Asian
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 15992
num of homozygotes: 0

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

Latino
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 11412
num of homozygotes: 0

African
type: Population
allele count: 0
allele frequency: 0.0e0
allele num: 9866
num of homozygotes: 0

BaseQRankSum
type: SiteQuality
SIO_000300: 4.02e0

MQRankSum
type: SiteQuality
SIO_000300: 2.45e-1

ReadPosRankSum
type: SiteQuality
SIO_000300: -2.7e-2

InbreedingCoeff
type: SiteQuality
SIO_000300: 0.0e0

VQSLOD
type: SiteQuality
SIO_000300: 4.6e0

QD
type: SiteQuality
SIO_000300: 1.616e1

FS
type: SiteQuality
SIO_000300: 0.0e0

ClippingRankSum
type: SiteQuality
SIO_000300: 2.39e-1

MQ
type: SiteQuality
SIO_000300: 6.0e1

DP
type: SiteQuality
SIO_000300: 1.647145e6