alphagenome-single-variant-analysis

What problem does it solve?

This Skill helps you evaluate how a single genetic variant may affect gene expression, chromatin accessibility, transcription factor binding, and splicing using the AlphaGenome API, producing interpretable plots and a report you can review for biological mechanisms.

Core Features & Use Cases

• Single-variant effect analysis (REF vs ALT): Generates predictions and Ref/Alt visual comparisons for regulatory and splicing-relevant modalities.
• Variant-driven discovery and tissue ranking: Supports a discovery scan and guides you to include disease-relevant tissues in the final interpretation.
• Mechanistic motif insight via ISM: Uses in-silico mutagenesis to identify likely disrupted motifs at the variant locus.
• Ontology term handling: Resolves and applies tissue/cell-type ontologies (e.g., UBERON/CL) and supports parsing variant formats such as chr:pos:ref>alt.

Quick Start

Use the alphagenome-single-variant-analysis skill to analyze a single variant in a tissue by generating AlphaGenome predictions, visualizations, and an output report.