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clinvar-database

Query ClinVar variant data via E-utilities API and FTP bulk downloads.

Updated Aug 23, 2026
Search Tags:#genomics#xml#vcf#eutilities#variant-interpretation#ftp#clinvar
One-click install
npx skills add https://github.com/Org-GAgent/result-interpreter --skill clinvar-database-org-gagent
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: clinvar-database
Source: https://github.com/Org-GAgent/result-interpreter/tree/main/.skills/scientific-skills/clinvar-database
Command: npx skills add https://github.com/Org-GAgent/result-interpreter --skill clinvar-database-org-gagent

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

ClinVar is NCBI's freely accessible archive of reports on relationships between human genetic variants and phenotypes, with supporting evidence. The database aggregates information about genomic variation and its relationship to human health, providing standardized variant classifications used in clinical genetics and research.

Core Features & Use Cases

  • Search ClinVar using the web interface at https://www.ncbi.nlm.nih.gov/clinvar/
  • Programmatic access via NCBI's E-utilities API for esearch, esummary, efetch, and elink
  • Download and process bulk data from FTP (XML, VCV, VCF, and tab-delimited formats)
  • Interpret classifications (Pathogenic, Likely Pathogenic, VUS, Benign, etc.) and review status
  • Link to related resources (PubMed, MedGen) and cross-reference data
  • Build pipelines and analytics using the provided reference documentation

Quick Start

Query ClinVar data by gene or condition and fetch summaries for analysis.

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 for pathogenic variants using E-utilities?▼

Programmatically query ClinVar for pathogenic variants using NCBI's E-utilities API by applying esearch, esummary, efetch, and elink operations to retrieve and filter variant interpretation data.

What bulk data formats are available for download from the ClinVar FTP site?▼

The ClinVar FTP site provides bulk data downloads in XML, VCV, VCF, and tab-delimited formats for integrating variant interpretations into bioinformatics pipelines.

Does this approach support retrieving ClinVar variant classifications and review status?▼

Yes, retrieving ClinVar variant classifications and review status is fully supported, allowing users to interpret standardized classifications like Pathogenic, Likely Pathogenic, VUS, and Benign.

Can I cross-reference ClinVar variant data with related medical resources?▼

You can cross-reference ClinVar variant data with related resources like PubMed and MedGen to link genomic variations to phenotypes and supporting evidence.

What is the best way to build a pipeline for downloading and processing ClinVar XML data?▼

Build pipelines for downloading and processing ClinVar XML data by utilizing the provided reference documentation alongside FTP bulk downloads and E-utilities API integration for automated analytics.

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