What do the star ratings in ClinVar mean?

Star ratings indicate the review status and level of confidence in a variant's classification; 4 stars represent practice guidelines, while 0 stars indicate no assertion criteria were provided.

Can I use this to annotate my own VCF files?

Yes, the skill provides specific workflows using tools like bcftools to download ClinVar VCFs and merge clinical significance data into your local variant sets.

Does this skill require an API key for NCBI?

While not strictly required, the skill recommends using an NCBI API key to increase request limits from 3 to 10 requests per second for more efficient data retrieval.

How do I search for pathogenic variants in a specific gene?

Use the skill to query the E-utilities API or web interface using patterns like 'GENENAME[gene] AND pathogenic[CLNSIG]' to isolate high-risk variants.

How does the skill handle conflicting variant interpretations?

It provides a resolution strategy that prioritizes entries with higher star ratings (expert panels) and evaluates submission dates to ensure the most current evidence is used.

ClinVar Database Navigator

Name: ClinVar Database Navigator
Author: Activer007

byActiver007

Ciencia de Datos y ML

Queries and interprets NCBI ClinVar data to identify genetic variant clinical significance and pathogenicity.

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The ClinVar Database skill provides specialized capabilities for interacting with NCBI's archive of human genetic variants and phenotypes. It enables users to search for variants via web or E-utilities API, interpret ACMG/AMP clinical significance classifications, and process bulk genomic data in XML, VCF, and tab-delimited formats. This tool is essential for researchers and bioinformaticians needing to annotate variant call sets, resolve conflicting interpretations, and integrate standardized clinical genetics data into their analysis pipelines.

Características Principales

High-confidence variant filtering using ClinVar review status star ratings
0 GitHub stars
Programmatic access via NCBI E-utilities API for automated queries
Bulk data processing workflows for VCF, XML, and tab-delimited files
Standardized interpretation of ACMG/AMP clinical significance classifications
Automated ClinVar VCF annotation patterns for genomic pipelines

Casos de Uso

Resolving conflicting variant interpretations using submission metadata and review status
Searching for expert-panel-reviewed variants associated with specific genes or diseases
Annotating a VCF file with clinical pathogenicity status and condition metadata

Acerca de

Características Principales

High-confidence variant filtering using ClinVar review status star ratings
0 GitHub stars
Programmatic access via NCBI E-utilities API for automated queries
Bulk data processing workflows for VCF, XML, and tab-delimited files
Standardized interpretation of ACMG/AMP clinical significance classifications
Automated ClinVar VCF annotation patterns for genomic pipelines

Casos de Uso

Resolving conflicting variant interpretations using submission metadata and review status
Searching for expert-panel-reviewed variants associated with specific genes or diseases
Annotating a VCF file with clinical pathogenicity status and condition metadata