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Genomic Variations

Term Description Type Properties Example Enum
caseLevelData caseLevelData reports about the variation instances observed in individual analyses. 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"
    }
}