Query Clinvar Agent Skill
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".
Install
one command, takes just this skill from the repositorynpx skills add https://github.com/BioTender-max/awesome-bio-agent-skills --skill query-clinvarThe instruction itself
6 sections, as written by the authorClinVar 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
from Bio import Entrez
import json
Entrez.email = "[email protected]"
# 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 variants: {search['Count']}")
if search['IdList']:
summaries = clinvar_summary(search['IdList'])
for uid in search['IdList']:
info = summaries['result'].get(str(uid), {})
title = info.get('title', 'N/A')
clinical_sig = info.get('clinical_significance', {}).get('description', 'N/A')
genes = info.get('genes', [{}])
gene = genes[0].get('symbol', 'N/A') if genes else 'N/A'
print(f"\nVariant: {title}")
print(f"Gene: {gene}")
print(f"Clinical significance: {clinical_sig}")
Common Search Patterns
- Pathogenic variants in gene:
BRCA1[gene] AND clinsig_pathogenic[prop] - By rsID:
rs6025[rsid] - By disease:
"breast cancer"[dis] AND clinsig_pathogenic[prop] - By chromosome region:
17[chr] AND 43000000:44000000[chrpos37] - Germline variants:
BRCA1[gene] AND origin_germline[prop]
Clinical Significance Categories
- Pathogenic, Likely pathogenic, Uncertain significance, Likely benign, Benign
Follow-up Suggestions
- "Want me to check the allele frequency in gnomAD?"
- "Should I look up this variant in Ensembl for more context?"
- "Want me to find all pathogenic variants in this gene?"
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How to use it
Take biotender-max/query-clinvar from the repository into ~/.claude/skills for personal
use, or into .claude/skills inside a project.
The agent identifies a skill by the name field in its header. Two skills with the
same name cannot sit side by side — one of them will be ignored.