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alphagenome-variant-impact-score

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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.

skills/alphagenome_variant_impact_score/SKILL.md

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# 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.