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clinvar-database

Retrieve clinical significance data for genetic variants from ClinVar.

1|Updated Mar 11, 2026
Search Tags:#genomics#data-analysis#eutilities#variant-interpretation#ftp#clinvar#vcf-annotation
One-click install
npx skills add https://github.com/SciMate-AI/scicli --skill clinvar-database-scimate-ai
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: clinvar-database
Source: https://github.com/SciMate-AI/scicli/tree/main/internal/skills/bundled/claude-scientific-skills/skills/clinvar-database
Command: npx skills add https://github.com/SciMate-AI/scicli --skill clinvar-database-scimate-ai

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

ClinVar data access and interpretation for research workflows: retrieve clinical significance, review statuses, and associated conditions for genetic variants.

Core Features & Use Cases

  • Programmatic access through E-utilities and FTP for bulk data
  • Query by gene, position, or condition and interpret clinical significance with ACMG/AMP-style terms
  • Data integration workflows: VCV/RCV/SCV formats, VCF annotations, and cross-referencing PubMed
  • Use cases include variant prioritization, study replication, and pipeline annotation

Quick Start

Query ClinVar for pathogenic BRCA1 variants using esearch and retrieve their summaries.

Frequently Asked Questions about clinvar-database

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

FAQPage Schema
How do I query ClinVar for pathogenic variants by gene or condition?▼

Query ClinVar by gene, position, or condition using NCBI E-utilities to retrieve and interpret clinical significance with ACMG/AMP-style terms directly from the database.

Can I download ClinVar data in bulk for variant annotation pipelines?▼

Yes, you can retrieve ClinVar data in bulk for variant annotation pipelines via FTP downloads. It supports processing XML, VCF, and tab-delimited formats.

What is the best way to cross-reference ClinVar data with PubMed literature?▼

The best way to cross-reference ClinVar data with PubMed literature is by utilizing programmatic access through E-utilities, allowing you to map variant significance to related publications.

Does this method support VCF annotation and RCV/SCV format integration?▼

Yes, it supports VCF annotation and data integration workflows, handling VCV, RCV, and SCV formats to process clinical significance and associated conditions for genetic variants.

When do I need to use ClinVar FTP bulk downloads instead of E-utilities?▼

You need ClinVar FTP bulk downloads instead of E-utilities when performing large-scale data integration workflows or pipeline annotations that require processing entire XML or VCF datasets locally.

How do I interpret ClinVar review statuses and clinical significance for genetic variants?▼

You interpret ClinVar review statuses and clinical significance by retrieving variant records, which provide ACMG/AMP-style terms and associated conditions for variant prioritization and study replication.

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