# Alphagenome Variant Impact Score

Score, annotate, and analyze the functional impact of genetic variants using...

- Repository: https://github.com/google-deepmind/science-skills (3377 stars)
- Category: Engineering
- License: Apache-2.0
- Last updated: 2026-10-23
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add google-deepmind/science-skills --skill alphagenome-variant-impact-score -g -a claude-code -y`
Codex: `npx skills add google-deepmind/science-skills --skill alphagenome-variant-impact-score -g -a codex -y`
Cursor: `npx skills add google-deepmind/science-skills --skill alphagenome-variant-impact-score -g -a cursor -y`
Gemini CLI: `npx skills add google-deepmind/science-skills --skill alphagenome-variant-impact-score -g -a gemini-cli -y`

## Description

Score, annotate, and analyze the functional impact of genetic variants using AlphaGenome Variant Impact (AVI) scores. Query variants in chr:pos:ref>alt format, annotate VCF/tabular callsets, perform saturation mutagenesis window scans (1-based closed chr:start-end), and extract GENCODE v46 GTF gene/exon/junction coordinates all via the AlphaGenome Atlas API.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# AlphaGenome Variant Impact (AVI) Analysis

Score and prioritize genetic variants using AlphaGenome Variant Impact (AVI)
models via `scripts/alphagenome_atlas_avi.py`.

> [!IMPORTANT] **Research Use Only & Clinical Safety Rules**: The AlphaGenome
> AVI Skill and the underlying AlphaGenome model/Atlas are **strictly research
> tools**. Access to outputs requires an AlphaGenome API key subject to terms of
> service prohibiting clinical use.
>
> 1.  **No Medical Advice or Clinical Diagnosis**: You **MUST NOT** provide
>     medical advice, clinical diagnoses, disease management strategies, or
>     treatment recommendations based on outputs from this skill or the
>     AlphaGenome Atlas.
> 2.  **Strict Molecular & Functional Framing**: A high AVI score reflects
>     **predicted molecular/functional impact** (e.g., disruption of splicing,
>     alteration of transcription factor binding, chromatin accessibility
>     changes, or coding consequences). Frame all findings in terms of molecular
>     mechanisms and biological annotations, never as clinical diagnoses or
>     medical conclusions.
> 3.  **No Diagnostic Leaps**: Never extrapolate high functional impact to
>     clinical disease causation, penetrance, or patient prognosis. If a user
>     asks a clinical or diagnostic question, explicitly clarify that
>     AlphaGenome is a research tool and restrict your answer to the predicted
>     molecular and functional effects.

> [!IMPORTANT] **Always Use AlphaGenome GENCODE v46 GTF
> (`scripts/alphagenome_atlas_avi.py gtf`) for Gene Annotations**: When
> retrieving gene models, transcript IDs, exon coordinates, CDS/UTR regions, or
> splice junction donor/acceptor boundaries, **always use the built-in
> `scripts/alphagenome_atlas_avi.py gtf` command**. Do **NOT** query external
> sources (e.g., Ensembl REST API, UCSC, external GTF databases, or NCBI) for
> gene annotations or transcript coordinates. This ensures that the annotations
> match the scores and website.

The rest: https://github.com/google-deepmind/science-skills/blob/HEAD/skills/alphagenome_variant_impact_score/SKILL.md