InternScience/variant-clinical-significance
skills/variant-clinical-significance/SKILL.md
Query NCBI ClinVar for variant clinical pathogenicity classification (Pathogenic/Benign/VUS), review status and associated diseases.
$ install --global
skillsauthnpx skillsauth add InternScience/scp variant-clinical-significanceInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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SKILL.md
- name:
- variant-clinical-significance
- description:
- Query NCBI ClinVar for variant clinical pathogenicity classification (Pathogenic/Benign/VUS), review status and associated diseases.
- license:
- MIT license
- skill-author:
- PJLab
ClinVar Clinical Significance
Usage
Tool Description
Query dbSNP refsnp API to extract ClinVar RCV clinical records for a variant.
API: GET https://api.ncbi.nlm.nih.gov/variation/v0/refsnp/{rsid_number}
Args:
rs_id (str): dbSNP rsID (e.g. "rs7412")
Return:
ClinVar RCV records: clinical significance (Pathogenic/Benign/VUS/drug-response etc.),
review status, associated diseases, accession numbers.
Query Example
import requests
rs_id = "rs7412"
# 通过 rsID 查询 dbSNP，提取 ClinVar RCV 记录
rsid_num = rs_id.replace("rs", "")
url = f"https://api.ncbi.nlm.nih.gov/variation/v0/refsnp/{rsid_num}"
resp = requests.get(url, timeout=30).json()
snapshot = resp.get("primary_snapshot_data", {})
for ann in snapshot.get("allele_annotations", []):
for clin in ann.get("clinical", []):
accession = clin.get("accession_version", "")
diseases = clin.get("disease_names", [])
significances = clin.get("clinical_significances", [])
review = clin.get("review_status", "")
print(f"[ClinVar RCV] {accession}: {significances}, diseases={diseases}, review={review}")
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