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clinvar-database

Query NCBI ClinVar for variant clinical significance and genomic evidence.

269|20|Updated Jun 13, 2026
Search Tags:#bioinformatics#genomics#ncbi#variant#clinvar#pathogenicity
One-click install
npx skills add https://github.com/NeuroAIHub/BrainPilot --skill clinvar-database-neuroaihub
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: clinvar-database
Source: https://github.com/NeuroAIHub/BrainPilot/tree/main/packages/skills/skills/18_Genetics_Genomics/clinvar-database
Command: npx skills add https://github.com/NeuroAIHub/BrainPilot --skill clinvar-database-neuroaihub

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This skill solves the challenge of manually searching and parsing complex clinical genomic data, providing a reliable way to fetch pathogenicity classifications and evidence for human variants.

Core Features & Use Cases

  • Variant Search: Identify variants by gene, genomic coordinates, or clinical attributes using NCBI Entrez syntax.
  • Clinical Evidence Retrieval: Fetch detailed submitter rationales, assertion criteria, and PubMed citations for specific variants.
  • Use Case: A researcher needs to find all pathogenic variants in the HBB gene to establish benchmark controls for a study; this skill automates the search and data aggregation process.

Quick Start

Use the clinvar-database skill to search for all pathogenic variants in the BRCA1 gene and save the results to a file named brca1_variants.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 pathogenicity labels for human genomic variants?▼

Use this Skill to query the NCBI ClinVar database for clinical significance and pathogenicity labels of human genomic variants. It supports gene-based, coordinate-based, and attribute-based searches to gather clinical evidence.

How do I find all pathogenic variants in a specific gene like BRCA1 or HBB?▼

You can perform a gene-based search using NCBI Entrez syntax to identify all pathogenic variants in a specific gene like BRCA1 or HBB. The skill automates the search and aggregates the clinical data into a structured output.

Why does my NCBI ClinVar API search return incomplete or missing genomic data?▼

Incomplete ClinVar API search results often occur due to rate-limiting or unhandled pagination. This skill implements robust rate-limiting, XML parsing, and pagination to ensure complete and deterministic genomic data retrieval.

Can I fetch PubMed citations and assertion criteria for clinical genomic variants?▼

Yes, you can fetch PubMed citations and assertion criteria for clinical genomic variants. The skill retrieves detailed submitter rationales and evidence directly from the NCBI ClinVar database for variant interpretation.

Do I need polite-http and python-dotenv to automate ClinVar database retrieval?▼

Yes, polite-http and python-dotenv are required dependencies. They manage environment variables and enforce robust HTTP rate-limiting to prevent query failures during automated ClinVar database retrieval.

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