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bio-clinical-databases-clinvar-lookup

Parse ClinVar CLNSIG, CLNREVSTAT, and CLNDN fields from REST API or local VCF.

Updated Aug 23, 2026
Search Tags:#bioinformatics#genomics#data-analysis#vcf#variant#clinvar#clinical-significance
One-click install
npx skills add https://github.com/stellaromics/fast-bioinfo --skill bio-clinical-databases-clinvar-lookup
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bio-clinical-databases-clinvar-lookup
Source: https://github.com/stellaromics/fast-bioinfo/tree/main/.claude/agents/spatial-analysis/skills/bio-clinical-databases-clinvar-lookup
Command: npx skills add https://github.com/stellaromics/fast-bioinfo --skill bio-clinical-databases-clinvar-lookup

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, cyvcf2, pandas.

What problem does it solve?

ClinVar variant data is essential for assessing clinical significance and disease associations, but retrieving accurate interpretations across APIs and local VCFs can be time-consuming without automation.

Core Features & Use Cases

  • REST-API lookups for ClinVar classifications, review status, and disease notes.
  • Local VCF querying with parsed CLNSIG/CLNREVSTAT/CLNDN, enabling offline workflows.
  • Use Case: Prioritize variants in diagnostic pipelines by retrieving pathogenicity and associated diseases for a given variant or gene.

Quick Start

Tell your AI agent to look up a ClinVar variant by ID or HGVS and return its clinical significance and disease associations.

Frequently Asked Questions about bio-clinical-databases-clinvar-lookup

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I query ClinVar clinical significance for genetic variants using REST API?▼

To query ClinVar clinical significance, you can look up variants by ID or HGVS notation via the REST API and retrieve structured results containing pathogenicity, review status, and disease names.

Can I parse CLNSIG and CLNDN fields from a local ClinVar VCF offline?▼

Yes, you can parse CLNSIG, CLNREVSTAT, and CLNDN fields directly from a local ClinVar VCF using cyvcf2, enabling offline workflows for variant annotation without requiring internet access.

What is the best way to batch annotate genetic variants with ClinVar disease associations?▼

Batch annotation of genetic variants with ClinVar disease associations is best handled by querying multiple variants or an entire gene to retrieve structured significance and disease name results in one pass.

Does this tool support retrieving review status and disease names for diagnostic pipelines?▼

Yes, it supports diagnostic pipelines by parsing the CLNREVSTAT field for review status and the CLNDN field for disease names, allowing you to prioritize variants based on clinical interpretation confidence.

Do I need pandas to process structured ClinVar variant data?▼

Pandas is required to process and structure the retrieved ClinVar variant data, transforming parsed VCF fields and API responses into organized tables for downstream data analysis workflows.

Why use a local VCF instead of the ClinVar REST API for variant lookups?▼

Using a local VCF instead of the ClinVar REST API is necessary for offline workflows or when processing high-volume batch annotations, avoiding network latency and API rate limits during genomic data analysis.

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