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clinvar-database

Retrieve ClinVar variant data via E-utilities and FTP in multiple formats.

1|Updated Jan 26, 2026
Search Tags:#genomics#vcf#eutilities#variant-interpretation#ftp#clinvar
One-click install
npx skills add https://github.com/Victory-Hugo/S2-Agent-Skill --skill clinvar-database-victory-hugo
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: clinvar-database
Source: https://github.com/Victory-Hugo/S2-Agent-Skill/tree/main/skills/databases/clinvar-database
Command: npx skills add https://github.com/Victory-Hugo/S2-Agent-Skill --skill clinvar-database-victory-hugo

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

This Skill provides programmatic access to ClinVar's records, enabling automated retrieval, interpretation, and integration of clinical significance data for genomic research workflows.

Core Features & Use Cases

  • API & FTP Access: Retrieve variant data via E-utilities (esearch, esummary, efetch, elink) or bulk downloads from the ClinVar FTP site.
  • Flexible Formats: Work with XML (VCV/RCV), VCF, and tab-delimited variant summaries to fit genomics pipelines.
  • Use Case: Build an annotation pipeline that queries BRCA1 pathogenic variants and aggregates summaries for downstream reporting.

Quick Start

Run a quick search for BRCA1 pathogenic variants: curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=clinvar&term=BRCA1[gene]+pathogenic[CLNSIG]&retmode=json"

  • For bulk retrieval, download ClinVar XML/VCF/tab-delimited files from ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/

Frequently Asked Questions about clinvar-database

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

FAQPage Schema
How do I programmatically query ClinVar variants for a specific gene like BRCA1?▼

Query ClinVar variants programmatically by calling NCBI E-utilities endpoints like esearch and efetch to retrieve clinical significance data for specific genes like BRCA1, returning results in JSON or XML format for automated genomics workflows.

What is the best way to bulk download ClinVar data for large-scale variant annotation?▼

Bulk download ClinVar data for large-scale variant annotation by retrieving files directly from the NCBI FTP site, accessing comprehensive variant summaries in VCF, XML, and tab-delimited formats to integrate into local genomics pipelines.

Can I retrieve ClinVar pathogenic variant interpretations in VCF format?▼

You can retrieve ClinVar pathogenic variant interpretations in VCF format. The database provides flexible data formats including VCF, XML (VCV/RCV), and tab-delimited variant summaries to fit various genomics annotation pipelines.

Which E-utilities functions are available for automated ClinVar data retrieval?▼

Available E-utilities functions for automated ClinVar data retrieval include esearch, esummary, efetch, and elink, enabling programmatic searching, summarizing, and fetching of clinical variant records directly into genomics workflows.

When should I use FTP downloads instead of E-utilities for accessing ClinVar records?▼

Use FTP downloads instead of E-utilities for accessing ClinVar records when you need large-scale data retrieval for bulk annotation workflows, whereas E-utilities are better suited for targeted queries of specific variant interpretations and clinical significance.

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