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bio-clinical-databases-clinvar-lookup

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Queries ClinVar for variant pathogenicity classifications, ClinGen VCEP curations, and somatic-vs-germline interpretations via REST API, weekly VCF, or bulk XML. Use when determining clinical significance, triangulating conflicting interpretations, or aggregating evidence against the ACMG/AMP framework with ClinGen SVI specifications.

skills/bioskills/bio-clinical-databases-clinvar-lookup/SKILL.md

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## Version Compatibility

Reference examples tested with: requests 2.31+, cyvcf2 0.30+, pandas 2.2+, bcftools 1.19+, Entrez Direct 21.0+, lxml 5.0+ (for v2 XML schema).

Before using code patterns, verify installed versions match. If versions differ:
- Python: `pip show <package>` then `help(module.function)` to check signatures
- CLI: `<tool> --version` then `<tool> --help` to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. ClinVar XML schema v2 (rolled out in 2024) replaces `<ClinVarSet>` with `<VariationArchive>` as the top-level anchor; XSLT or parsers targeting the legacy element silently emit zero records.

# ClinVar Lookup and Clinical-Significance Triangulation

**'Look up the clinical significance of this variant'** -> Retrieve ClinVar VCV-level aggregate, SCV-level submissions, ClinGen Variant Curation Expert Panel (VCEP) overrides, and conflict-resolution status.