Can I use this for clinical diagnosis?

No, this is a research and analysis tool; all clinical decisions should be verified and made by qualified genetics professionals.

How do I handle conflicting interpretations?

The skill provides a multi-step resolution strategy focusing on review status, submission dates, and evidence examination to weigh competing classifications.

How does this skill help with VCF files?

It provides standardized commands and scripts using tools like bcftools and Python to annotate VCF files with ClinVar clinical significance data.

Does this skill support API access?

Yes, it includes comprehensive guidance for using NCBI's E-utilities API to programmatically search, fetch, and summarize variant records.

What are ClinVar star ratings?

Star ratings (0-4) indicate the review status and level of confidence in a variant's classification, with expert panels and practice guidelines carrying the most weight.

ClinVar Database Assistant

Name: ClinVar Database Assistant
Author: BbgnsurfTech

byBbgnsurfTech

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Data Science & ML

Queries and interprets NCBI ClinVar data to provide standardized genetic variant classifications and clinical significance evidence.

About

This skill empowers Claude to interact with the NCBI ClinVar archive, a critical resource for genomic medicine that aggregates reports on human genetic variants and phenotypes. It provides specialized guidance on searching variants by gene or condition, interpreting complex pathogenicity classifications like Pathogenic, Benign, and VUS, and accessing data through E-utilities APIs or bulk FTP downloads. Whether you are annotating VCF files for a bioinformatics pipeline or resolving conflicting variant interpretations, this skill ensures best practices in clinical genetics data handling and analysis.

Key Features

Bulk data processing for XML, VCF, and tab-delimited formats
3 GitHub stars
Interpretation of ACMG/AMP clinical significance classifications
Guidance on resolving conflicting variant interpretations
Standardized variant search by gene, position, or condition
Programmatic access via NCBI E-utilities API and curl

Use Cases

Filtering and prioritizing pathogenic variants in specific gene panels
Automating bulk downloads of ClinVar datasets for local bioinformatics pipelines
Annotating genomic VCF files with clinical significance for research

About

Key Features

Bulk data processing for XML, VCF, and tab-delimited formats
3 GitHub stars
Interpretation of ACMG/AMP clinical significance classifications
Guidance on resolving conflicting variant interpretations
Standardized variant search by gene, position, or condition
Programmatic access via NCBI E-utilities API and curl

Use Cases

Filtering and prioritizing pathogenic variants in specific gene panels
Automating bulk downloads of ClinVar datasets for local bioinformatics pipelines
Annotating genomic VCF files with clinical significance for research