clinvar

ClinVar Evidence

Use this skill when the user asks about clinical labels, carrier findings, pathogenic/likely pathogenic entries, VUS, conflicting classifications, drug response, risk-factor labels, or ClinVar-derived discovery.

Goal

Build a candidate landscape from exact ClinVar matches. Use candidate_inventory as variant-level provenance evidence and candidate_review_groups as the carrier/condition review inventory.

Convention: See skills/conventions/evidence-quality.md.

Contract

• ClinVar matches provide exact/static evidence for source-backed interpretation.
• Exact matching requires the optional build-specific library clinvar-grch38 or clinvar-grch37.
• Candidate inventories are variant-level evidence, not interpretation.
• Candidate review groups are review targets. A heterozygous P/LP group can be carrier-relevance evidence; it is not a carrier-status conclusion.
• clinvar.scan_candidates returns an evidence view, grouped support, warnings, and coverage; use those fields rather than inferring priority from prose.
• By default, clinvar.scan_candidates includes P/LP, conflicting, VUS, risk/association/protective, drug-response, and benign ClinVar groups.
• If ClinVar matches are missing, clinvar.scan_candidates materializes them from the Active Genome Index before building the candidate inventory.
• VUS, conflicts, and low-review assertions are downgraded unless reviewed source evidence supports a stronger claim.
• Drug-response rows use pharmacogenomic source context before actionability is implied.

Cross-Capability Synthesis

A scope-limited result from this capability is not a final user-facing answer when other Genomi capabilities can contribute orthogonal evidence to the same question. Returning "cannot answer" while applicable capabilities remain unexamined is a host-agent failure mode.

Tools

clinvar.match_variants

Materialize exact ClinVar matches for comparable Active Genome Index variants using the installed build-specific ClinVar library.