clinvar-json

small variants:

"clinvar":[
   {
      "id":"VCV000036581.3",
      "reviewStatus":"reviewed by expert panel",
      "significance":[
         "benign"
      ],
      "refAllele":"G",
      "altAllele":"A",
      "lastUpdatedDate":"2020-03-01",
      "isAlleleSpecific":true
   },
   {
      "id":"RCV000030258.4",
      "variationId":"VCV000036581.3",
      "reviewStatus":"reviewed by expert panel",
      "alleleOrigins":[
         "germline"
      ],
      "refAllele":"G",
      "altAllele":"A",
      "phenotypes":[
         "Lynch syndrome"
      ],
      "medGenIds":[
         "C1333990"
      ],
      "omimIds":[
         "120435"
      ],
      "significance":[
         "benign"
      ],
      "lastUpdatedDate":"2017-05-01",
      "isAlleleSpecific":true
   }
]

large variants:

"clinvar":[
   {
      "chromosome":"1", 
      "begin":629025, 
      "end":8537745, 
      "variantType":"copy_number_loss", 
      "id":"RCV000051993.4", 
      "variationId":"VCV000058242.1", 
      "reviewStatus":"criteria provided, single submitter", 
      "alleleOrigins":[
         "not provided"
      ], 
      "phenotypes":[
         "See cases"
      ], 
      "significance":[
         "pathogenic"
      ], 
      "lastUpdatedDate":"2022-04-21", 
      "pubMedIds":[
         "21844811"
      ]
   },
   {
      "id":"VCV000058242.1",
      "reviewStatus":"criteria provided, single submitter",
      "significance":[
         "pathogenic"
      ],
      "lastUpdatedDate":"2022-04-21"
   },
        ......
]

Field	Type	Notes
id	string	ClinVar ID
variationId	string	ClinVar VCV ID
variantType	string	variant type
reviewStatus	string	see possible values below
alleleOrigins	string array	see possible values below
refAllele	string
altAllele	string
phenotypes	string array
medGenIds	string array	MedGen IDs
omimIds	string array	OMIM IDs
orphanetIds	string array	Orphanet IDs
significance	string array	see possible values below
lastUpdatedDate	string	yyyy-MM-dd
pubMedIds	string array	PubMed IDs
isAlleleSpecific	bool	true when the current variant alternate allele matches the ClinVar alternate allele

reviewStatus:

• no assertion provided
• no assertion criteria provided
• criteria provided, single submitter
• practice guideline
• classified by multiple submitters
• criteria provided, conflicting interpretations
• criteria provided, multiple submitters, no conflicts
• no interpretation for the single variant

alleleOrigins:

• unknown
• other
• germline
• somatic
• inherited
• paternal
• maternal
• de-novo
• biparental
• uniparental
• not-tested
• tested-inconclusive

significance:

• uncertain significance
• not provided
• benign
• likely benign
• likely pathogenic
• pathogenic
• drug response
• histocompatibility
• association
• risk factor
• protective
• affects
• conflicting data from submitters
• other
• no interpretation for the single variant
• conflicting interpretations of pathogenicity