# Bio Clinical Databases Clinvar Lookup

Query ClinVar for variant pathogenicity classifications, review status, and disease...

- Repository: https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills (3090 stars)
- Category: Writing
- License: see repository
- Last updated: 2026-07-21
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-clinical-databases-clinvar-lookup -g -a claude-code -y`
Codex: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-clinical-databases-clinvar-lookup -g -a codex -y`
Cursor: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-clinical-databases-clinvar-lookup -g -a cursor -y`
Gemini CLI: `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-clinical-databases-clinvar-lookup -g -a gemini-cli -y`

## Description

Query ClinVar for variant pathogenicity classifications, review status, and disease associations via REST API or local VCF. Use when determining clinical significance of variants for diagnostic or research purposes.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

## Version Compatibility

Reference examples tested with: Entrez Direct 21.0+, bcftools 1.19+

Before using code patterns, verify installed versions match. If versions differ:
- Python: `pip show <package>` then `help(module.function)` to check signatures
- CLI: `<tool> --version` then `<tool> --help` to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed
package and adapt the example to match the actual API rather than retrying.

# ClinVar Lookup

## REST API Queries

**Goal:** Retrieve ClinVar pathogenicity classifications and disease associations for variants via REST API.

**Approach:** Query NCBI E-utilities endpoints with variant IDs, gene symbols, or HGVS notation and parse JSON responses.

**"Look up this variant in ClinVar"** → Query ClinVar database for clinical significance, review status, and disease associations.
- Python: `requests.get()` against NCBI E-utilities (requests)
- CLI: `esearch`/`efetch` (Entrez Direct)

### Query by Variant ID

```python
import requests

def query_clinvar_by_id(variation_id):
    '''Query ClinVar by variation ID'''
    url = f'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi'
    params = {
        'db': 'clinvar',
        'id': variation_id,
        'retmode': 'json'
    }
    response = requests.get(url, params=params)
    return response.json()

result = query_clinvar_by_id('16609')
```

### Search by Gene

```python
def search_clinvar_gene(gene_symbol, pathogenic_only=False):
    '''Search ClinVar for variants in a gene'''
    url = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi'

    term = f'{gene_symbol}[gene]'
    if pathogenic_only:
        term += ' AND pathogenic[clinical_significance]'

    params = {
        'db': 'clinvar',
        'term': term,
        'retmax': 500,
        'retmode': 'json'
    }
    response = requests.get(url, params=params)
    return response.json()
```

### Search by HGVS

The rest: https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/blob/HEAD/skills/bio-clinical-databases-clinvar-lookup/SKILL.md