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.