clinvar-database

Query ClinVar for variant clinical significance via E-utilities and FTP bulk downloads.

52|6|Updated Nov 24, 2025

Search Tags:#genomics #ClinVar #RCV #VCV #EFETCH #CLI utils

Ready to run

npx skills add https://github.com/ovachiever/droid-tings --skill clinvar-database

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: clinvar-database
Source: https://github.com/ovachiever/droid-tings/tree/main/skills/clinvar-database
Command: npx skills add https://github.com/ovachiever/droid-tings --skill clinvar-database

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

ClinVar data is essential for understanding clinical significance of genetic variants; this skill helps query ClinVar via E-utilities, download bulk data, and annotate variant calls.

Core Features & Use Cases

ClinVar search & web/API access: esearch/esummary/efetch workflows
Clinical significance interpretation: reference to ClinVar sign and review status
Data acquisition: FTP bulk downloads for XML/VCV/VCF formats
Variant annotation pipelines: integration of ClinVar data into pipelines

Quick Start

Retrieve a specific pathogenic BRCA1 variant using the E-utilities endpoint: python skills/clinvar-database/references/api_reference.md -- Not actual; Use curl to query esearch.

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 variant clinical significance using E-utilities?▼

Query ClinVar clinical significance using E-utilities APIs (esearch, esummary, efetch) to retrieve variant data by gene, condition, or variant identifier. Results include VCV/RCV records with ACMG/AMP classifications and review status for interpretation.

Can I annotate VCF files with ClinVar variant data?▼

Yes. Integrate ClinVar data into VCF annotation pipelines by retrieving clinical significance, review status, and cross-references via E-utilities or FTP bulk downloads, then map results to variant calls for complete pathogenicity annotation.

What data formats does ClinVar support for bulk downloads?▼

ClinVar bulk downloads provide XML VCV/RCV records, VCF format, and tab-delimited outputs via FTP. Each format preserves clinical significance, review status, and literature linkage needed for variant interpretation workflows.

How do I access ClinVar data programmatically without manual downloads?▼

Use E-utilities API endpoints (esearch, esummary, efetch, elink) for programmatic access to ClinVar variant records, enabling integration into automated pipelines for gene-centric, condition-centric, or variant-centric searches.

What's the difference between VCV and RCV records in ClinVar?▼

VCV (Variation) records represent unique variants with aggregated clinical significance; RCV (RCVaccession) records represent individual ClinVar submissions with specific review status and evidence. Both are accessible via E-utilities for comprehensive variant interpretation.

Do I need prior knowledge of ACMG/AMP classifications to use ClinVar data?▼

ClinVar provides ACMG/AMP classification data directly, so you can query and apply existing classifications without prior expertise. The Skill handles retrieval and annotation; interpretation guidelines are embedded in the returned records.