Cross-References (variation_xref)

Overview

The variation_xref table is created by the clinvar_ingest.variation_identity stored procedure. It extracts cross-reference (XRef) entries from ClinVar variation records, providing links to external databases that have catalogued the same or related variants.

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Fields

Field	Type	Description
variation_id	string	ClinVar variation identifier.
db	string	The name of the external database (e.g., ClinGen, dbSNP, OMIM, UniProtKB). Parsed from the XRef list in the variation's XML content.
id	string	The identifier assigned to this variant in the external database (e.g., a ClinGen allele registry ID, an rsID).
type	string	The type or category of the cross-reference as provided by ClinVar.

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Row Granularity

One row per variation_id + external reference combination. A single variation may have zero, one, or many cross-references across different external databases.

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Notes

The cross-references are parsed from the XRefList element of each variation's content using the clinvar_ingest.parseXRefs UDF. Downstream, the variation_identity table consumes these cross-references to build a mappings array, where ClinGen references are assigned a closeMatch relation and all other databases are assigned relatedMatch.