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clinvar-database

Retrieve clinical significance and evidence for human genomic variants from NCBI ClinVar.

2.7k|283|Updated May 13, 2026
Search Tags:#genomics#variant interpretation#clinvar#clinical evidence#ncbi eutils#api rate limiting
One-click install
npx skills add https://github.com/google-deepmind/science-skills --skill clinvar-database-google-deepmind
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: clinvar-database
Source: https://github.com/google-deepmind/science-skills/tree/main/skills/clinvar_database
Command: npx skills add https://github.com/google-deepmind/science-skills --skill clinvar-database-google-deepmind

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires scienceskillscommon, python-dotenv, and includes scripts (resource) components.

What problem does it solve?

ClinVar variant queries are hard to execute reliably, paginate completely, and translate raw records into usable clinical labels and evidence for human genomic variants.

Core Features & Use Cases

  • Clinical significance discovery: Find clinical significance, review status (star-rating), and phenotypes for one or many ClinVar variant IDs.
  • Evidence-grade deep dives: Pull full clinical evidence including submitter rationales, assertion criteria, PubMed citation IDs, and structured condition/ontology links.
  • Variant search at scale: Use NCBI Entrez query syntax to search by gene symbols, coordinates, or clinical attributes with deterministic pagination and controllable result limits.

Quick Start

Use the ClinVar Database skill to search for BRCA1 variants by running: uv run scripts/clinvar_api.py search --query "BRCA1[gene]" --output results.json.

Frequently Asked Questions about clinvar-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I retrieve clinical significance and review status for human genomic variants from ClinVar?▼

Retrieve clinical significance and review status for human genomic variants from ClinVar by querying gene symbols or coordinate ranges via NCBI Entrez search syntax. The skill extracts structured records including phenotypes and detailed clinical evidence submissions.

Can I pull full clinical evidence including PubMed citations and submitter rationales for ClinVar variants?▼

Yes, you can pull full clinical evidence for ClinVar variants including submitter rationales, assertion criteria, PubMed citation IDs, and structured condition and ontology links through per-variant evidence retrieval with pagination support.

How do I search ClinVar variants at scale by gene symbols or clinical attributes?▼

Search ClinVar variants at scale by constructing NCBI Entrez query syntax targeting gene symbols, coordinate ranges, or clinical attributes. The skill manages deterministic pagination and controllable result limits for large batch queries.

Do I need an NCBI API key to query the ClinVar database?▼

An NCBI API key is optional but recommended to increase rate limits. The skill authenticates by loading an NCBI_API_KEY from a user .env file and uses an NCBI E-utilities wrapper for built-in rate limiting and XML or JSON parsing.

What are the limitations of using NCBI E-utilities for variant interpretation queries?▼

NCBI E-utilities impose API rate limiting that affects variant interpretation query throughput. The skill mitigates this with a wrapper and optional NCBI API key authentication, but deterministic pagination and controllable result limits are required for large dataset extraction.

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