Home / Skills / annotating-variants
annotating-variants
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, consequence, missense, gnomAD, allele frequency, GRCh38, rsID, transcript. Pairs adjacent to OpenMed: combine a
Why this score
This repo hosts 10 skills, so its 5,697 stars are split between them (about 570 each) for scoring.
Popularity score: 77/100 from public GitHub signals only. It shows how widely used and maintained this is, not how well it works. Not included yet: the fake-star check. The security scan is shown separately and doesn't change the score. How we rank
Security
Scanned Oct 20, 2026 at commit 8440bdac5962, with Cisco's open-source skill-scanner.
What its code does:
- Makes network requestsSKILL.md:54 and 1 more
Web addresses in its code:
- rest.ensembl.orgSKILL.md:75
These are the sites named in the code, so it's where your data could go. It isn't a complete list: code can build addresses while it runs, and a few of these may be links rather than calls. Whatever you send also goes to the AI model you use.
A scan lists patterns in the code. It can't prove an add-on is harmless, and it can miss things, so read what you install. How we scan
Alternatives
Other makers' add-ons that do the same job, next to this one.
| Name | Score | Stars | Context | Updated |
|---|---|---|---|---|
| This oneannotating-variants maziyarpanahi/openmed · Skill | 77 | ★ 5.7k | ≈155 always | 16d ago |
| annotating-task-lineage astronomer/agents · Skill Both about annotating and annotate | 66 | ★ 454 | ≈65 always | 21d ago |
| scenario-ad-variants scenario-labs/skills · Skill Both about variant and ad | 69 | ★ 1.1k | ≈91 always | 16d ago |
| alphagenome-variant-impact-score google-deepmind/science-skills · Skill Both about variant and annotate | 75 | ★ 3.3k | ≈34 always | 20d ago |
| batch-montage-variants 0xsline/OpenChatCut · Skill Both about variant | 74 | ★ 2.5k | ≈36 always | 17d ago |