How can I query variants by gene using this skill?

You can use search patterns like 'BRCA1[gene]' or 'pathogenic[CLNSIG]' via web interface instructions or programmatically using the E-utilities API examples provided.

Can this skill help with VCF annotation?

Yes, it provides specific commands for tools like bcftools to download ClinVar VCFs and annotate your own variant call sets with clinical data.

What is the ClinVar Database skill for Claude?

It is a specialized capability for Claude Code designed to search, interpret, and process human genetic variant data from NCBI's ClinVar archive.

What do the ClinVar star ratings signify?

Star ratings represent review status: 0 stars indicate no assertion criteria, while 4 stars represent the highest confidence levels, such as practice guidelines.

How does the skill handle conflicting variant interpretations?

It provides a multi-step resolution strategy including checking star ratings, reviewing submission dates, and consulting expert panel classifications.

ClinVar Genomic Database

Name: ClinVar Genomic Database
Author: x-cmd

byx-cmd

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Data Science & ML

Queries and interprets NCBI ClinVar genetic variant data to provide clinical significance classifications and genomic annotations.

This skill enables Claude to interact with the NCBI ClinVar database, the primary archive for human genetic variation and its relationship to health phenotypes. It provides specialized guidance on querying variants by gene or position using E-utilities, interpreting ACMG/AMP pathogenicity classifications, and processing large-scale genomic data from VCF, XML, and tab-delimited formats. It is essential for bioinformaticians and researchers needing to automate variant annotation, resolve conflicting interpretations, or build local genomic data pipelines while adhering to best practices in clinical genetics.

Key Features

01Programmatic access to NCBI E-utilities API for real-time variant querying

02Conflict resolution strategies for disparate variant pathogenicity interpretations

03Standardized interpretation of ACMG/AMP clinical significance and star-rated review statuses

04Integration with bioinformatic tools like bcftools and Python for variant annotation

058 GitHub stars

06Bulk data processing workflows for VCF, XML, and tab-delimited ClinVar datasets

Use Cases

01Annotating patient VCF files with high-confidence clinical significance ratings

02Building automated pipelines to track updates in variant classifications for specific gene panels

03Researching the clinical evidence and phenotypes associated with specific genetic mutations

Key Features

01Programmatic access to NCBI E-utilities API for real-time variant querying

02Conflict resolution strategies for disparate variant pathogenicity interpretations

03Standardized interpretation of ACMG/AMP clinical significance and star-rated review statuses

04Integration with bioinformatic tools like bcftools and Python for variant annotation

058 GitHub stars

06Bulk data processing workflows for VCF, XML, and tab-delimited ClinVar datasets

Use Cases

01Annotating patient VCF files with high-confidence clinical significance ratings

02Building automated pipelines to track updates in variant classifications for specific gene panels

03Researching the clinical evidence and phenotypes associated with specific genetic mutations