How do I access ClinVar programmatically with this skill?

Use the NCBI E-utilities API endpoints (esearch, esummary, efetch) via curl or libraries like Biopython. The skill provides specific command patterns and rate limit guidance for these tools.

How should I handle conflicting variant interpretations in ClinVar?

The skill suggests prioritizing high star ratings (expert panels), checking submission dates for updated evidence, and reviewing population frequency data like gnomAD to contextualize the conflict.

What do the ClinVar star ratings indicate?

Ratings (0-4 stars) represent the review status and confidence level of a classification. They range from 'No assertion criteria' (0 stars) to 'Expert panel review' (3 stars) and 'Practice guidelines' (4 stars).

Can I use this skill to annotate VCF files?

Yes, the skill provides specific workflows and bcftools commands for downloading ClinVar VCF files for GRCh37/GRCh38 and annotating your own genomic variant call sets.

ClinVar Database

Name: ClinVar Database
Author: Microck

byMicrock

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数据科学与机器学习

Accesses and interprets the NCBI ClinVar archive to identify genomic variant clinical significance and pathogenicity classifications.

关于

The ClinVar Database skill enables developers and researchers to programmatically query the NCBI ClinVar archive for human genetic variants and their associated health phenotypes. It provides specialized guidance on searching by gene or condition, interpreting standardized ACMG/AMP pathogenicity classifications (Pathogenic, Benign, VUS), and accessing data via E-utilities API or bulk FTP downloads. This skill is essential for annotating VCF files, resolving conflicting interpretations, and integrating clinical genomics data into bioinformatics pipelines for genomic medicine.

主要功能

Standardized pathogenicity interpretation using ACMG/AMP guidelines
Bulk data processing workflows for XML, VCF, and tab-delimited formats
Conflict resolution strategies for variant interpretations using review star ratings
Programmatic access via NCBI E-utilities API and Biopython
Advanced search query construction by gene, chromosome, or disorder
81 GitHub stars

使用场景

Annotating variant call sets (VCFs) with high-confidence clinical significance data
Building automated pipelines to monitor and track variant classification updates over time
Cross-referencing genomic variants with specific diseases or phenotypic conditions for research

关于

主要功能

Standardized pathogenicity interpretation using ACMG/AMP guidelines
Bulk data processing workflows for XML, VCF, and tab-delimited formats
Conflict resolution strategies for variant interpretations using review star ratings
Programmatic access via NCBI E-utilities API and Biopython
Advanced search query construction by gene, chromosome, or disorder
81 GitHub stars

使用场景

Annotating variant call sets (VCFs) with high-confidence clinical significance data
Building automated pipelines to monitor and track variant classification updates over time
Cross-referencing genomic variants with specific diseases or phenotypic conditions for research