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annotating-variants

Annotate and normalize genomic variants from VCF files, rsIDs, and HGVS descriptions with consequences and population frequencies.

5.0k|615|Updated Oct 4, 2025
Search Tags:#genomics#vcf#oncology#gnomad#vep#variant annotation#hgvs
One-click install
npx skills add https://github.com/maziyarpanahi/openmed --skill annotating-variants
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: annotating-variants
Source: https://github.com/maziyarpanahi/openmed/tree/main/skills/annotating-variants
Command: npx skills add https://github.com/maziyarpanahi/openmed --skill annotating-variants

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This Skill transforms raw VCF variants, rsIDs, and HGVS descriptions into normalized genomic records with predicted consequences, transcript effects, and population frequency context, while helping connect molecular findings to clinical narratives.

Core Features & Use Cases

  • Variant Annotation: Annotate variants using Ensembl VEP REST, offline VEP, SnpEff, or ANNOVAR workflows.
  • HGVS Normalization: Map transcript-level HGVS descriptions to genomic coordinates while accounting for reference builds and transcript selection.
  • Frequency and Clinical Context: Link variants to gnomAD allele frequencies and combine molecular findings with OpenMed-extracted genes, phenotypes, and oncology context.
  • Use Case: Given a GRCh38 VCF from a tumor sequencing workflow, normalize the variants, predict their consequences, attach gnomAD frequencies, and associate relevant findings with extracted clinical context.

Quick Start

Use the annotating-variants skill to normalize and annotate the HGVS variant ENST00000269305.9:c.215C>G, then report its consequence, affected transcripts, protein change, and available gnomAD frequency.

Frequently Asked Questions about annotating-variants

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

FAQPage Schema
How do I annotate VCF variants with gnomAD frequencies and predicted consequences?▼

Annotating VCF variants involves normalizing alleles and applying tools like Ensembl VEP REST, offline VEP, SnpEff, or ANNOVAR to predict consequences and attach gnomAD population frequencies across GRCh38 or GRCh37 builds.

Can I map transcript-level HGVS descriptions to genomic coordinates?▼

Mapping transcript-level HGVS descriptions to genomic coordinates requires transcript-aware HGVS handling and consistent reference builds to accurately normalize variants and identify affected transcripts and protein changes.

Does this variant annotation workflow support oncology tumor sequencing data?▼

Variant annotation workflows support oncology applications by normalizing VCF data from tumor sequencing, predicting consequences, attaching gnomAD frequencies, and associating molecular findings with extracted oncology context.

What is the best way to normalize genomic variants from rsIDs for clinical sequencing review?▼

Normalizing genomic variants from rsIDs for clinical sequencing review requires using open annotators or user-supplied offline databases to predict transcript effects, attach population frequency context, and ensure consistent reference builds.

Do I need offline databases to annotate variants when open annotators are unavailable?▼

When open annotators are unavailable, you need user-supplied offline databases to annotate variants. The workflow supports offline VEP and offline database approaches to maintain annotation and normalization capabilities without external API access.

How does variant annotation prioritize phenotype-linked findings in molecular reports?▼

Variant annotation prioritizes phenotype-linked findings by combining molecular results with OpenMed-extracted genes and phenotypes, connecting predicted consequences and gnomAD frequencies with clinical narratives to support molecular report generation.

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