Are there rate limits when using the ClinVar API?

NCBI limits E-utilities to 3 requests per second without a key, but this skill provides guidance on using API keys to increase that limit to 10 requests per second.

How does this skill handle conflicting variant interpretations?

It provides a multi-step resolution strategy that prioritizes review status star ratings, submission dates, and expert panel classifications to identify the most reliable interpretation.

Does it support programmatic access to NCBI?

Yes, it includes detailed instructions for utilizing NCBI's E-utilities API (esearch, esummary, efetch) and accessing bulk data via the ClinVar FTP site.

Can I use this skill to annotate VCF files?

Yes, the skill provides specific workflows and command-line examples using bcftools and Python to annotate VCF files with ClinVar clinical significance data.

ClinVar Database

Name: ClinVar Database
Author: Sologa

bySologa

Data Science & ML

Queries and interprets genetic variant clinical significance data from the NCBI ClinVar database.

About

The ClinVar Database skill enables researchers and bioinformatics developers to interact seamlessly with NCBI's archive of human genetic variants and their relationships to phenotypes. It provides specialized guidance for querying variants by gene or condition, interpreting pathogenicity classifications using ACMG/AMP guidelines, and accessing data programmatically via E-utilities or bulk FTP downloads. This skill is essential for annotating VCF files, resolving interpretation conflicts, and building automated genomic analysis pipelines that require high-confidence clinical evidence.

Key Features

Query NCBI ClinVar by gene, condition, variant, or clinical significance
0 GitHub stars
Interpret ACMG/AMP classifications including review status star ratings
Resolution strategies for conflicting variant interpretations
VCF annotation and processing for genomic medicine pipelines
Programmatic access via E-utilities API and automated FTP downloads

Use Cases

Automating the retrieval of pathogenic variant lists for specific genes
Annotating variant call sets (VCF) with clinical significance and metadata
Building local genomic databases using monthly XML and VCF releases

About

Key Features

Query NCBI ClinVar by gene, condition, variant, or clinical significance
0 GitHub stars
Interpret ACMG/AMP classifications including review status star ratings
Resolution strategies for conflicting variant interpretations
VCF annotation and processing for genomic medicine pipelines
Programmatic access via E-utilities API and automated FTP downloads

Use Cases

Automating the retrieval of pathogenic variant lists for specific genes
Annotating variant call sets (VCF) with clinical significance and metadata
Building local genomic databases using monthly XML and VCF releases