# 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".

- **Type:** Skill
- **Install:** `agentstack add skill-cheatthegod-biohermes-query-clinvar`
- **Verified:** Yes — security-reviewed for prompt injection and unsafe behavior
- **Seller:** [cheatthegod](https://agentstack.voostack.com/s/cheatthegod)
- **Installs:** 0
- **Category:** [Agent Skills](https://agentstack.voostack.com/c/agent-skills)
- **Latest version:** 0.1.0
- **License:** MIT
- **Upstream author:** [cheatthegod](https://github.com/cheatthegod)
- **Source:** https://github.com/cheatthegod/BioHermes/tree/main/optional-skills/bioinformatics/query-clinvar

## Install

```sh
agentstack add skill-cheatthegod-biohermes-query-clinvar
```

Requires the [AgentStack CLI](https://agentstack.voostack.com/docs/cli). Works with Claude Code, Cursor, and any MCP-compatible agent.

## About

# 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

```python
from Bio import Entrez
import json

Entrez.email = "bioclaw@example.com"

# 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?"

## Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

- **Author:** [cheatthegod](https://github.com/cheatthegod)
- **Source:** [cheatthegod/BioHermes](https://github.com/cheatthegod/BioHermes)
- **License:** MIT

Install and usage instructions live in the source repository linked above.

## Pricing

- **Free** — Free

## Security capabilities

Automated source analysis of v0.1.0 — what this tool can access:

- **Network access:** no
- **Filesystem access:** no
- **Shell / process execution:** no
- **Environment & secrets:** no
- **Dynamic code execution:** no

*"Yes" means the capability is present in the source — more access means more to trust, not that it is unsafe.*


## Versions

- **0.1.0** — security scan: passed — Imported from the upstream source.

## Links

- Listing page: https://agentstack.voostack.com/l/skill-cheatthegod-biohermes-query-clinvar
- Seller: https://agentstack.voostack.com/s/cheatthegod
- Browse the marketplace: https://agentstack.voostack.com/browse

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