Does it support both GRCh37 and GRCh38 builds?

Yes, the skill includes specific workflows for downloading and processing ClinVar VCF data mapped to both major human genome assemblies.

How does this skill access ClinVar data?

It uses a combination of NCBI E-utilities API for live queries, FTP downloads for bulk data processing, and standardized web search patterns for specific variant lookups.

How does it handle conflicting variant interpretations?

The skill provides systematic strategies to evaluate review status (star ratings), submission dates, and evidence levels to help researchers resolve conflicting pathogenicity assertions.

Can I use this for clinical diagnosis?

No, this is a research tool for data analysis and scientific discovery; clinical interpretations should always be validated by a certified genetics professional.

ClinVar Database Assistant

Name: ClinVar Database Assistant
Author: jimmc414

byjimmc414

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324

Data Science & ML

Queries the NCBI ClinVar database to retrieve, interpret, and process human genetic variant clinical significance data.

About

This skill integrates NCBI's ClinVar database directly into the Claude environment, allowing users to search for genetic variants by gene or condition, interpret pathogenicity classifications (P/LP/VUS), and process genomic data. It provides standardized workflows for programmatic access via E-utilities API, bulk data retrieval from FTP servers, and variant call set (VCF) annotation. Designed for genomic medicine and bioinformatics, it helps automate the complex process of cross-referencing variant data with clinical evidence, review status, and expert panel classifications.

Key Features

Annotate VCF files with clinical significance and review status using bcftools
324 GitHub stars
Automate bulk data downloads and parsing from NCBI FTP servers
Resolve conflicting variant interpretations based on evidence star ratings
Interpret clinical significance classifications using ACMG/AMP guidelines
Query ClinVar via E-utilities API and advanced web search patterns

Use Cases

Building automated bioinformatics pipelines for VCF annotation and filtering
Researching the clinical significance and supporting evidence for specific human phenotypes
Identifying high-confidence pathogenic variants in specific genes like BRCA1 or CFTR

About

Key Features

Annotate VCF files with clinical significance and review status using bcftools
324 GitHub stars
Automate bulk data downloads and parsing from NCBI FTP servers
Resolve conflicting variant interpretations based on evidence star ratings
Interpret clinical significance classifications using ACMG/AMP guidelines
Query ClinVar via E-utilities API and advanced web search patterns

Use Cases

Building automated bioinformatics pipelines for VCF annotation and filtering
Researching the clinical significance and supporting evidence for specific human phenotypes
Identifying high-confidence pathogenic variants in specific genes like BRCA1 or CFTR