genomicVariations defaultSchema
| Term | Description | Type | Properties | Example | Enum |
|---|---|---|---|---|---|
| caseLevelData | array | alleleOrigin, analysisId, biosampleId, clinicalInterpretations, id, individualId, phenotypicEffects, runId, zygosity | NA | NA | |
| frequencyInPopulations | NA | array | frequencies, source, sourceReference, version | NA | NA |
| identifiers | NA | object | clinvarVariantId, genomicHGVSId, proteinHGVSIds, transcriptHGVSIds, variantAlternativeIds | NA | NA |
| molecularAttributes | NA | object | aminoacidChanges, geneIds, genomicFeatures, molecularEffects | NA | NA |
| variantInternalId | Reference to the internal variant ID. This represents the primary key/identifier of that variant inside a given Beacon instance. Different Beacon instances may use identical id values, referring to unrelated variants. Public identifiers such as the GA4GH Variant Representation Id (VRSid) MUST be returned in the identifiers section. A Beacon instance can, of course, use the VRSid as their own internal id but still MUST represent this then in the identifiers section. |
string | NA | var00001, v110112 | NA |
| variantLevelData | NA | object | clinicalInterpretations, phenotypicEffects | NA | NA |
| variation | NA | oneOf | LegacyVariation, MolecularVariation, SystemicVariation | NA | NA |
Examples¶
These are examples extracted directly from the GitHub repository.
{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"variantInternalId": "GRCh37-1-55505652-G-A",
"variation": {
"alternateBases": "A",
"location": {
"interval": {
"end": {
"type": "Number",
"value": 5505653
},
"start": {
"type": "Number",
"value": 5505652
},
"type": "SequenceInterval"
},
"sequence_id": "refseq:NC_000001.10",
"type": "SequenceLocation"
},
"variantType": "SNP"
}
}
{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"variantInternalId": "GRCh37-1-55505652-G-A",
"variation": {
"location": {
"interval": {
"end": {
"type": "Number",
"value": 5505653
},
"start": {
"type": "Number",
"value": 5505652
},
"type": "SequenceInterval"
},
"sequence_id": "refseq:NC_000001.10",
"type": "SequenceLocation"
},
"state": {
"sequence": "A",
"type": "SequenceState"
},
"type": "Allele"
}
}
{
"$schema": "https://json-schema.org/draft/2020-12/schema",
"frequencyInPopulations": [
{
"frequencies": [
{
"alleleFrequency": 2.939e-05,
"population": "European (non-Finish)"
},
{
"alleleFrequency": 0,
"population": "Other"
}
],
"source": "gnomaD Genomes",
"sourceReference": "https://gnomad.broadinstitute.org/",
"version": "v3.1.1"
},
{
"frequencies": [
{
"alleleFrequency": 9e-05,
"population": "Total"
},
{
"alleleFrequency": 6e-05,
"population": "European"
},
{
"alleleFrequency": 0,
"population": "African"
}
],
"source": "ALFA",
"sourceReference": "https://www.ncbi.nlm.nih.gov/snp/docs/gsr/alfa/",
"version": "20201027095038"
}
],
"identifiers": {
"clinVarIds": [
"434136",
"VCV000440707.6"
],
"genomicHGVSId": "NC_000001.11:g.55039979G>A",
"proteinHGVSIds": [
"NP_777596.2:p.Glu48Lys"
],
"transcriptHGVSIds": [
"NM_174936.4:c.142G>A"
],
"variantAlternativeIds": [
"dbSNP:rs3975092470",
"ClinGen: CA340482854"
]
},
"molecularAttributes": {
"aminoacidChanges": [
"E48K"
],
"geneIds": [
"PCSK9",
"LRG_275"
],
"molecularEffects": [
{
"id": "ENSGLOSSARY:0000150",
"label": "Missense variant"
}
]
},
"variantInternalId": "var123",
"variantLevelData": {
"clinicalInterpretations": [
{
"category": {
"id": "MONDO:0000001",
"label": "disease or disorder"
},
"clinicalRelevance": "pathogenic",
"conditionId": "famchol1",
"effect": {
"id": "MONDO:0007750",
"label": "Familial hypercholesterolemia 1"
}
},
{
"category": {
"id": "MONDO:0000001",
"label": "disease or disorder"
},
"clinicalRelevance": "uncertain significance",
"conditionId": "famchol3",
"effect": {
"id": "MONDO:0011369",
"label": "hypercholesterolemia, autosomal dominant, 3"
}
}
]
},
"variation": {
"alternateBases": "A",
"location": {
"interval": {
"end": {
"type": "Number",
"value": 55039980
},
"start": {
"type": "Number",
"value": 55039979
},
"type": "SequenceInterval"
},
"sequence_id": "refseq:NC_000001.11",
"type": "SequenceLocation"
},
"referenceBases": "G",
"variantType": "SNP"
}
}