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clinvar-database

Query NCBI ClinVar for clinical significance and evidence of human genomic variants.

1|Updated Aug 31, 2026
Search Tags:#genomics#E-utilities#ncbi#ClinVar#variant classification#pathogenicity#clinical evidence
One-click install
npx skills add https://github.com/nguyenhungtran18/skill-and-tool-tracker --skill clinvar-database-nguyenhungtran18
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: clinvar-database
Source: https://github.com/nguyenhungtran18/skill-and-tool-tracker/tree/main/skills/clinvar_database
Command: npx skills add https://github.com/nguyenhungtran18/skill-and-tool-tracker --skill clinvar-database-nguyenhungtran18

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve? Looking up the clinical significance of human genomic variants requires navigating NCBI ClinVar's complex E-utilities API, strict rate limits, and inconsistent XML schemas. This Skill wraps that complexity into four simple commands so you can retrieve pathogenicity classifications, review statuses, and clinician evidence without writing API code. ## Core Features & Use Cases - Variant Search & Counting: Search ClinVar by gene symbol, chromosome position, or clinical significance using Entrez syntax, with automatic pagination for complete result sets. - Interpretation Summaries: Retrieve clinical significance labels, star ratings (review status), phenotypes, and molecular consequences for rapid variant screening. - Full Clinical Evidence: Fetch per-submitter classifications, curator notes, assertion criteria, PubMed citations, and GRCh38 genomic coordinates for deep dives. - Use Case: A clinical genomics researcher needs all Pathogenic variants in the HBB gene with their genomic coordinates and supporting lab evidence. The Skill counts matches, fetches all variant IDs, screens summaries, and pulls full evidence records into JSON files. ## Quick Start Ask the AI to find all pathogenic variants in the BRCA1 gene from ClinVar and summarize their clinical significance and review status.

Frequently Asked Questions about clinvar-database

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

FAQPage Schema
How do I search ClinVar for pathogenic variants in a gene?▼

Run the search command with an Entrez query like "HBB[gene] AND pathogenic[clinsig]" via the clinvar_api.py script. It automatically paginates through all matching results and returns variant IDs with total and fetched counts in a JSON file.

How to get clinical significance and review status for a ClinVar variant?▼

Use the summary command with one or more ClinVar Variation IDs. It returns clinical_significance, review_status (star rating), last_evaluated date, phenotypes, genes, variation type, and molecular consequences for each variant.

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

An NCBI_API_KEY is optional but recommended. Without it, the rate limit is 3 requests per second; with a key it rises to 10. You can register for a free key at the NCBI account settings page and set it in your .env file.

Why am I getting HTTP 429 errors from the ClinVar API?▼

HTTP 429 means you exceeded the NCBI rate limit of 3 requests per second without an API key. Pause execution, obtain a free NCBI API key, add it as NCBI_API_KEY to your .env file, and retry the query.

When should I not use ClinVar for variant analysis?▼

ClinVar does not provide population allele frequencies (use gnomAD), normal gene function and inheritance patterns (use OMIM), mechanistic predictions for novel mutations (use AlphaGenome), or patient surveillance schedules (use GeneReviews).

How do I get GRCh38 genomic coordinates for a ClinVar variant?▼

Use the evidence command, which parses the VCV XML and returns allele_info with chromosome, position, reference, and alternate alleles from the GRCh38 SequenceLocation. If coordinates are imprecise, resolve them via the dbsnp-database skill using the rsID.

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