annotating-variants SKILL.md skillA
annotating-variants from maziyarpanahi/openmed is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add maziyarpanahi/openmed/annotating-variants@v1.0Pins v1.0 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- maziyarpanahi/openmed
- Path
skills/annotating-variants/SKILL.md- Versions recorded
- 1
- Latest version
- v1.0, committed Jul 20, 2026
- Size
- 8,512 bytes
- Repository stars
- 5,784
- License
- Apache-2.0
Annotates VCF variants and normalizes HGVS nomenclature with public, license-free annotators (Ensembl VEP REST, VEP/SnpEff/ANNOVAR offline) and links variants to gnomAD population frequencies and the clinical context OpenMed extracts. Use when the user wants to predict variant consequences, map HGVS to genomic coordinates, annotate a VCF, attach allele frequencies, or pair variants with phenotype/oncology context. Trigger keywords: VCF, HGVS, variant annotation, VEP, SnpEff, ANNOVAR…
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# Annotating variants & normalizing HGVS Turn raw genomic variants — VCF rows, rsIDs, or **HGVS** strings — into annotated, consequence-predicted records, and link them to the **clinical context** OpenMed extracts from text (genes, variants, oncology findings, phenotype). The workhorse for a quick, no-install annotation is the **Ensembl VEP REST API**; for scale, run **VEP**, **SnpEff**, or **ANNOVAR** offline. These annotators are **free and license-permissive**. Restricted clinical interpretation databases (e.g. licensed HGMD) are **user-supplied** — this skill sticks to open resources (Ensembl, gnomAD, ClinVar). ## When to use - You have a VCF / HGVS / rsID and need consequence predictions (missense, stop-gain, splice), affected transcripts, and protein change. - You need to **normalize HGVS** to genomic coordinates (and back) on a known build (GRCh38 by default; GRCh37 via the dedicated endpoint). - You want **gnomAD** population allele frequencies to flag common vs rare. - You are pairing molecular findings with the phenotype/oncology context that OpenMed pulls from notes or literature. ## Quick start (real Ensembl VEP REST call) …
Read the whole file at its exact version.
How to install
mdr add maziyarpanahi/openmed/annotating-variants@sha256:b5f6c5fe74e14f75The line at the top of this page pins the label v1.0, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_kl366vvoxfhtkmfz)
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Versions
The registry has recorded 1 version of this file, committed on Jul 20, 2026.
Audit of the latest version
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Source
maziyarpanahi/openmed · 5,784 stars · license Apache-2.0 · pushed 2026-11-07 · branch master
API
GET https://markdownregistry.com/api/v1/artifacts/art_kl366vvoxfhtkmfz GET https://markdownregistry.com/api/v1/resolve?ref=maziyarpanahi/openmed/annotating-variants GET https://markdownregistry.com/api/v1/blob/b5f6c5fe74e14f757191b886bf0da895e0432957b782eaa29f8835300079cfff
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Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.