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ClinVar

ClinVar is the most recognizable public archive for germline and somatic clinical significance claims, so it is often the first source people want when they ask whether a variant is pathogenic, uncertain, or well reviewed. It matters because the labels are familiar to labs, researchers, and reviewers even when the upstream submission evidence is messy.

BioMCP retrieves the current NCBI Variation Archive record directly for an explicit clinvar section (and for all) after MyVariant.info resolves a numeric ClinVar Variation ID. The default variant card remains a fast indirect summary. If direct retrieval fails, a usable MyVariant.info snapshot is returned as a clearly degraded fallback with its available evaluation date and submitter count.

What BioMCP exposes

Command What BioMCP gets from this source Integration note
get variant <id> Base variant card with ClinVar-backed significance signals when present Indirect summary through MyVariant.info; no direct ClinVar request
get variant <id> clinvar Current condition-specific RCV aggregates and separate current SCV submissions Direct NCBI ClinVar, with MyVariant.info fallback
search variant -g <gene> --significance <value> Variant search filtered by ClinVar significance labels Search rows can surface ClinVar-derived review and significance hints

Example commands

biomcp get variant rs113488022

Returns a base variant card that can include ClinVar-backed summary fields when they are available.

biomcp get variant rs113488022 clinvar

Returns the current direct ClinVar record with condition-specific aggregates and each current submission kept separate. Domains such as germline, somatic clinical impact, and oncogenicity are not combined into a consensus.

biomcp get variant "BRAF V600E" clinvar

Returns the same ClinVar section for a gene-plus-protein variant ID.

biomcp search variant -g BRCA1 --significance pathogenic --limit 5

Returns variant rows filtered by ClinVar significance labels.

API access

NCBI E-utilities EFetch (db=clinvar, rettype=vcv, Variation ID lookup) powers explicit clinvar and all requests. The Variant guide covers the broader workflow that hosts this section.

No credential is required. An optional NCBI_API_KEY is sent to NCBI E-utilities when configured and enables the provider's higher request budget.

Official source

ClinVar is the official NCBI archive for clinical variant interpretations.