What problem does it solve? Prioritizing which genetic variants are functionally important from large VCF callsets or candidate lists is slow and requires integrating many genomic data modalities. This Skill scores variants with calibrated AlphaGenome Variant Impact (AVI) Phred scores, decomposes predictions into 18 biological feature attributions, and ranks candidates so researchers can focus on the highest-impact variants. ## Core Features & Use Cases - Variant Querying & Scoring: Query single or multiple variants in chr:pos:ref>alt format to get Phred scores, quantiles, top percentiles, and 18-modality feature importances with optional track-level provenance. - VCF/Tabular Annotation: Annotate VCF, CSV, TSV, or Parquet callsets in Ensembl VEP CSQ format, rank top candidates, and export machine-readable results. - Saturation Mutagenesis Scans: Score all possible SNVs across a genomic window (chr:start-end) to find functional hotspots. - GENCODE v46 Gene Annotations: Extract exon boundaries, CDS/UTR segments, and canonical or exon-skipping splice junction coordinates for genes and transcripts. - Use Case: Given a VCF of 1,000 rare variants from a sequencing study, annotate the entire callset, filter to variants with Phred >= 20 (top 1% genome-wide), and inspect whether top hits are driven by splicing, chromatin accessibility, or conservation. ## Quick Start Ask the assistant to query the variant chr9:128225994:G>A with the AlphaGenome AVI skill and report its Phred score, top percentile, and top contributing biological modality with an Atlas deep-link.
