query-clinvar
Query ClinVar for clinical variant significance. Use when user asks about variant pathogenicity, genetic variants, clinical significance, or disease-causing mutations. Triggers on "clinvar", "pathogenic", "variant significance", "clinical significance", "disease variant", "mutation pathogenicity".
npx skills add BioTender-max/awesome-bio-agent-skills --skill query-clinvar --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.
# ClinVar Clinical Variant Database Query NCBI ClinVar for clinical significance of genetic variants. ## When to Use - User asks if a variant is pathogenic - User wants to find known pathogenic variants in a gene - User asks about clinical significance of SNPs - User wants variant-disease associations ## How to Execute ```python from Bio import Entrez import json Entrez.email = "bioclaw@example.com" # 1. Search ClinVar def search_clinvar(query, max_results=10): handle = Entrez.esearch(db="clinvar", term=query, retmax=max_results) record = Entrez.read(handle) handle.close() return record # 2. Fetch variant details def fetch_clinvar(id_list): ids = ",".join(str(i) for i in id_list) handle = Entrez.efetch(db="clinvar", id=ids, rettype="vcv", retmode="xml") result = handle.read() handle.close() return result # 3. Summary for ClinVar IDs def clinvar_summary(id_list): ids = ",".join(str(i) for i in id_list) handle = Entrez.esummary(db="clinvar", id=ids, retmode="json") result = json.loads(handle.read()) handle.close() return result # Example: Find pathogenic BRCA1 variants search = search_clinvar("BRCA1[gene] AND clinsig_pathogenic[prop]", max_results=5) print(f"Total pathogenic BRCA1 va
- When to Use
- How to Execute
- Common Search Patterns
- Clinical Significance Categories
- Follow-up Suggestions
What does the query-clinvar skill do?
Query ClinVar for clinical variant significance. Use when user asks about variant pathogenicity, genetic variants, clinical significance, or disease-causing mutations. Triggers on "clinvar", "pathogenic", "variant significance", "clinical significance", "disease variant", "mutation pathogenicity".
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill query-clinvar --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.