bio-clinical-databases-clinvar-lookup
Query ClinVar for variant pathogenicity classifications, review status, and disease associations via REST API or local VCF. Use when determining clinical significance of variants for diagnostic or research purposes.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-clinical-databases-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: Entrez Direct 21.0+, bcftools 1.19+ 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 Lookup ## REST API Queries **Goal:** Retrieve ClinVar pathogenicity classifications and disease associations for variants via REST API. **Approach:** Query NCBI E-utilities endpoints with variant IDs, gene symbols, or HGVS notation and parse JSON responses. **"Look up this variant in ClinVar"** → Query ClinVar database for clinical significance, review status, and disease associations. - Python: `requests.get()` against NCBI E-utilities (requests) - CLI: `esearch`/`efetch` (Entrez Direct) ### Query by Variant ID ```python import requests def query_clinvar_by_id(variation_id): '''Query ClinVar by variation ID''' url = f'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi' params = { 'db': 'clinvar
- Version Compatibility
- REST API Queries
- Query by Variant ID
- Search by Gene
- Search by HGVS
- Local ClinVar VCF
- Download ClinVar VCF
- Query Local ClinVar with cyvcf2
- Clinical Significance Categories
- Review Status Stars
- Parse ClinVar INFO Fields
- Batch Annotation with bcftools
- Related Skills
GRCh38 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 GRCh37 wget https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/clinvar.vcf.gz Annotate VCF with ClinVar bcftools annotate \ input.vcf.gz \
What does the bio-clinical-databases-clinvar-lookup skill do?
Query ClinVar for variant pathogenicity classifications, review status, and disease associations via REST API or local VCF. Use when determining clinical significance of variants for diagnostic or research purposes.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-clinical-databases-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 FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 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.