clinvar-database

Retrieve and interpret genetic variant data from the NCBI ClinVar database.

Updated Dec 17, 2025

Search Tags:#genomics #data retrieval #variant interpretation #clinvar #genetic databases

Ready to run

npx skills add https://github.com/robotlearning123/claude-scientific-skills --skill clinvar-database-robotlearning123

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: clinvar-database
Source: https://github.com/robotlearning123/claude-scientific-skills/tree/main/scientific-skills/clinvar-database
Command: npx skills add https://github.com/robotlearning123/claude-scientific-skills --skill clinvar-database-robotlearning123

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires biopython, requests, pandas, numpy, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill empowers users to easily search, interpret, and download data from NCBI ClinVar, streamlining access to genomic variant and phenotype relationships for genomic medicine.

Core Features & Use Cases

ClinVar Search: Access ClinVar's vast database of variants and clinical significance through both a web interface and programmatically via E-utilities API.
Variant Interpretation: Understand ACMG/AMP pathogenicity classifications and review status star ratings.
Data Retrieval: Access ClinVar data in various formats like XML, VCF, and tab-delimited for integration with research and clinical workflows.

Quick Start

Search for pathogenic variants in BRCA1 gene using the ClinVar skill.

Frequently Asked Questions about clinvar-database

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

FAQPage Schema

How do I query NCBI ClinVar for genetic variant data programmatically?▼

To query NCBI ClinVar for genetic variant data, you can retrieve information programmatically using the E-utilities API. This approach facilitates efficient variant querying and data retrieval for genomic research workflows.

How do I interpret ACMG/AMP pathogenicity classifications and review status star ratings from ClinVar?▼

Interpreting ACMG/AMP pathogenicity classifications and review status star ratings from ClinVar involves analyzing the clinical significance of genetic variants. This skill provides variant interpretation capabilities to understand these pathogenicity classifications and review statuses.

Can I download ClinVar variant data in VCF and XML formats for clinical workflows?▼

Yes, you can download ClinVar variant data in VCF, XML, and tab-delimited formats. This data retrieval capability ensures seamless integration of variant and phenotype relationships into your clinical workflows.

Does the ClinVar data retrieval process require XML parsing capabilities?▼

Yes, retrieving and processing ClinVar data requires XML parsing capabilities to handle the E-utilities API responses. The skill also relies on biopython, requests, pandas, and numpy to manage the genomic data retrieval workflows.

What is the best way to search for pathogenic variants in the BRCA1 gene using ClinVar?▼

The best way to search for pathogenic variants in the BRCA1 gene is to use the ClinVar search functionality via the E-utilities API. This enables precise querying and classification analysis of specific genetic variants.