Positions
Each position represents one row of the VCF file. Each position contains a samples section and a variants section. Reference and alternate alleles shown here matches the VCF content exactly.
The samples section lists the sample-specific information, such as genotype, in the same order as they appear in the VCF and in the JSON header above.
The variants section provides annotations for each alternate allele that appear in the VCF row. This includes allele-specific annotation from external data sources as well as transcript-level annotation. Reference and alternate alleles shown here are shown in their most shortened representation. For example, padding bases have been removed and the variant are left-aligned.
"positions": [
{
"chromosome": "chr1",
"position": 1043248,
"refAllele": "C",
"altAlleles": [
"T"
],
"quality": 441.42,
"filters": [
"PASS"
],
"strandBias": -425.94,
"cytogeneticBand": "1p36.33",
"samples": [
{
"genotype": "0/1",
"variantFrequencies": [
0.537
],
"totalDepth": 54,
"genotypeQuality": 99,
"alleleDepths": [
25,
29
]
}
],
"variants": [
{
"vid": "1-1043248-C-T",
"chromosome": "chr1",
"begin": 1043248,
"end": 1043248,
"refAllele": "C",
"altAllele": "T",
"variantType": "SNV",
"hgvsg": "NC_000001.11:g.1043248C>T",
"phylopScore": 0.1,
"clinvar": [
{
"id": "RCV000872112.1",
"variationId": 263161,
"reviewStatus": "criteria provided, single submitter",
"alleleOrigins": [
"germline"
],
"refAllele": "C",
"altAllele": "T",
"phenotypes": [
"not provided"
],
"medGenIds": [
"CN517202"
],
"significance": [
"likely benign"
],
"lastUpdatedDate": "2019-12-17",
"pubMedIds": [
"28492532"
],
"isAlleleSpecific": true
},
{
"id": "VCV000263161.2",
"reviewStatus": "criteria provided, multiple submitters, no conflicts",
"significance": [
"likely benign"
],
"refAllele": "C",
"altAllele": "T",
"lastUpdatedDate": "2019-12-17",
"isAlleleSpecific": true
}
],
"dbsnp": [
"rs116586548"
],
"globalAllele": {
"globalMinorAllele": "T",
"globalMinorAlleleFrequency": 0.004393
},
"gnomad": {
"coverage": 38,
"allAf": 0.000681,
"allAn": 264462,
"allAc": 180,
"allHc": 0,
"afrAf": 0.006216,
"afrAn": 23648,
"afrAc": 147,
"afrHc": 0,
"amrAf": 0.000689,
"amrAn": 33404,
"amrAc": 23,
"amrHc": 0,
"easAf": 0,
"easAn": 18830,
"easAc": 0,
"easHc": 0,
"finAf": 0,
"finAn": 22870,
"finAc": 0,
"finHc": 0,
"nfeAf": 5e-05,
"nfeAn": 120576,
"nfeAc": 6,
"nfeHc": 0,
"asjAf": 0.000304,
"asjAn": 9882,
"asjAc": 3,
"asjHc": 0,
"sasAf": 0,
"sasAn": 28456,
"sasAc": 0,
"sasHc": 0,
"othAf": 0.000147,
"othAn": 6796,
"othAc": 1,
"othHc": 0,
"maleAf": 0.000564,
"maleAn": 143614,
"maleAc": 81,
"maleHc": 0,
"femaleAf": 0.000819,
"femaleAn": 120848,
"femaleAc": 99,
"femaleHc": 0,
"controlsAllAf": 0.000626,
"controlsAllAn": 113456,
"controlsAllAc": 71
},
"oneKg": {
"allAf": 0.004393,
"afrAf": 0.016641,
"amrAf": 0,
"easAf": 0,
"eurAf": 0,
"sasAf": 0,
"allAn": 5008,
"afrAn": 1322,
"amrAn": 694,
"easAn": 1008,
"eurAn": 1006,
"sasAn": 978,
"allAc": 22,
"afrAc": 22,
"amrAc": 0,
"easAc": 0,
"eurAc": 0,
"sasAc": 0
},
"primateAI": [
{
"hgnc": "AGRN",
"scorePercentile": 0.12
}
],
"revel": {
"score": 0.136
},
"spliceAI": [
{
"hgnc": "AGRN",
"acceptorGainScore": 0.1,
"acceptorGainDistance": 23,
"acceptorLossScore": 0,
"acceptorLossDistance": -9,
"donorGainScore": 0,
"donorGainDistance": -5,
"donorLossScore": 0,
"donorLossDistance": 16
}
],
"topmed": {
"allAf": 0.002055,
"allAn": 125568,
"allAc": 258,
"allHc": 1
},
"transcripts": [
{
"transcript": "ENST00000379370.6",
"source": "Ensembl",
"bioType": "protein_coding",
"codons": "cCg/cTg",
"aminoAcids": "P/L",
"cdnaPos": "1444",
"cdsPos": "1394",
"exons": "8/36",
"proteinPos": "465",
"geneId": "ENSG00000188157",
"hgnc": "AGRN",
"consequence": [
"missense_variant"
],
"hgvsc": "ENST00000379370.6:c.1394C>T",
"hgvsp": "ENSP00000368678.2:p.(Pro465Leu)",
"isCanonical": true,
"polyPhenScore": 0.065,
"polyPhenPrediction": "benign",
"proteinId": "ENSP00000368678.2",
"siftScore": 0.05,
"siftPrediction": "tolerated"
},
{
"transcript": "NM_198576.3",
"source": "RefSeq",
"bioType": "protein_coding",
"codons": "cCg/cTg",
"aminoAcids": "P/L",
"cdnaPos": "1444",
"cdsPos": "1394",
"exons": "8/36",
"proteinPos": "465",
"geneId": "375790",
"hgnc": "AGRN",
"consequence": [
"missense_variant"
],
"hgvsc": "NM_198576.3:c.1394C>T",
"hgvsp": "NP_940978.2:p.(Pro465Leu)",
"isCanonical": true,
"polyPhenScore": 0.065,
"polyPhenPrediction": "benign",
"proteinId": "NP_940978.2",
"siftScore": 0.05,
"siftPrediction": "tolerated"
}
]
}
]
}
],