variant-clinical-significance
Query NCBI ClinVar for variant clinical pathogenicity classification (Pathogenic/Benign/VUS), review status and associated diseases.
Best use case
variant-clinical-significance is best used when you need a repeatable AI agent workflow instead of a one-off prompt.
Query NCBI ClinVar for variant clinical pathogenicity classification (Pathogenic/Benign/VUS), review status and associated diseases.
Teams using variant-clinical-significance should expect a more consistent output, faster repeated execution, less prompt rewriting.
When to use this skill
- You want a reusable workflow that can be run more than once with consistent structure.
When not to use this skill
- You only need a quick one-off answer and do not need a reusable workflow.
- You cannot install or maintain the underlying files, dependencies, or repository context.
Installation
Claude Code / Cursor / Codex
Manual Installation
- Download SKILL.md from GitHub
- Place it in
.claude/skills/variant-clinical-significance/SKILL.mdinside your project - Restart your AI agent — it will auto-discover the skill
How variant-clinical-significance Compares
| Feature / Agent | variant-clinical-significance | Standard Approach |
|---|---|---|
| Platform Support | Not specified | Limited / Varies |
| Context Awareness | High | Baseline |
| Installation Complexity | Unknown | N/A |
Frequently Asked Questions
What does this skill do?
Query NCBI ClinVar for variant clinical pathogenicity classification (Pathogenic/Benign/VUS), review status and associated diseases.
Where can I find the source code?
You can find the source code on GitHub using the link provided at the top of the page.
SKILL.md Source
# ClinVar Clinical Significance
## Usage
### Tool Description
```tex
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
```python
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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