bio-clinical-databases-clinvar-lookup
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.
npx skills add BioTender-max/awesome-bio-agent-skills --skill clinvar-lookup --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## 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. - Python (REST): `requests.get()` against the E-utilities `clinvar` database - Python (local VCF): `cyvcf2.VCF('clinvar.vcf.gz')` for batch queries against the weekly snapshot - CLI: `bcftools
- Version Compatibility
- Star Ratings and the Override Hierarchy
- ClinGen Variant Curation Expert Panels (VCEPs)
- ACMG/AMP, ClinGen SVI Specifications, and the Bayesian Point System
- Conflicting Interpretations and Conflict Resolution
- Decision Tree by Query Scenario
- REST API Query (E-utilities)
- Local VCF Query (Weekly Snapshot)
- ClinGen Allele Registry (CA IDs): The Real Cross-Database Anchor
- Per-Operation Failure Modes
- Reconciliation: When Sources Disagree
- Quantitative Thresholds and Operational Conventions
- ClinVar Somatic vs Germline: 2024 Tripartite
- Common Errors
mkdir -p clinvar/$(date +%Y%m); cd clinvar/$(date +%Y%m) wget https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz wget https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz.tbi bcftools annotate \ input.vcf.gz -O z -o annotated.vcf.gz bcftools index -t annotated.vcf.gz
What does the bio-clinical-databases-clinvar-lookup skill do?
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.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill clinvar-lookup --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.