Query Clinvar

biotender-max/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".

698 tokens

context cost

the whole folder, loaded on every use

files

instructions only

copies elsewhere

how many repositories repackaged it

132

stars on the repo

on the repository, not the skill itself

Install

one command, takes just this skill from the repository

npx skills add https://github.com/BioTender-max/awesome-bio-agent-skills --skill query-clinvar

The instruction itself

6 sections, as written by the author

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

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?"

How to use it

Copy the folder

Take biotender-max/query-clinvar from the repository into ~/.claude/skills for personal use, or into .claude/skills inside a project.

Check the name does not clash

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.