GDM AlphaGenome Variant Analysis skill

Qualified idgoogle-deepmind/science-skills@1.2.1

Predicts a non-coding genomic variant's effect on gene expression, chromatin accessibility, histone marks, and transcription-factor binding via Google DeepMind's hosted AlphaGenome API.

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Overview

The alphagenome-single-variant-analysis skill from Google DeepMind's Science Skills collection. Given a variant in chr:pos:ref>alt form (or a gene/region query), it calls the AlphaGenome API to predict effects on RNA-seq expression, DNase chromatin accessibility, ChIP histone marks, and transcription-factor binding, and its own SKILL.md description names the workflow's actual purpose -- 'non-coding variant effects, pathogenicity, clinical significance, disease associations' -- alongside sibling skills in the same repository for clinvar_database, gnomad_database, and dbsnp_database lookups, confirmed live via direct fetch of the skills directory listing. Verified live via direct fetch of the skill's SKILL.md and its internal project documentation (a biological-interpretation and pre-report reasoning checklist), plus the repository's published technical report on the Science Skills collection. Terms check: the repository's root LICENSE is Apache-2.0 (confirmed by direct fetch and by plugin.json's license field), and the repository's own SKILL_LICENSES.md separately documents that individual skills reference third-party data sources (AlphaGenome, ClinVar, gnomAD, etc.) carrying their own terms of use -- a data-usage-terms disclosure, not a code-licence divergence, so Apache-2.0 is recorded as this entry's license without qualification. The collection is built and documented primarily for Google's Antigravity harness (distributed via the open Agent Skills standard's npx skills add); Antigravity has no matching entry in this registry's closed harness vocabulary (schemas/vocab/harnesses.json), so host_runtimes is omitted below rather than mapped to an unverified value. No slug collision with any existing entry in this registry.

Details

Licence
Apache-2.0
Version
1.2.1
Category
Variant interpretation
Homepage
https://github.com/google-deepmind/science-skills/tree/main/skills/alphagenome_single_variant_analysis
Repository
https://github.com/google-deepmind/science-skills
Maintainers
Susheel Varma (@susheel, GA4GH AI Workstream / Sage Bionetworks)
Keywords
alphagenomevariant-effect-predictionregulatory-genomicsgoogle-deepmindclinvargnomad

Publisher

Published by
Google DeepMind (GitHub organisation) profile ↗
Upstream name
science-skills
Upstream version
1.2.1 (Git tag)
Version date

Safety classification

No safety classification has been submitted for this entry.

What the safety levels mean

Skill

Human oversight
required
Provenance logging
No
Evaluation criteria
https://storage.googleapis.com/deepmind-media/papers/google_deepmind_science_skills_for_antigravity_towards_efficient_and_reliable_scientific_workflows.pdf
Source
https://github.com/google-deepmind/science-skills.git (skills/alphagenome_single_variant_analysis)

Inputs

  • variant (string) — A genomic variant in chr:pos:ref>alt format, or a gene symbol/genomic region for de-novo annotation.
  • tissue_or_cell_type (string) — Optional UBERON/CL ontology term scoping the prediction to a tissue or cell-type context.

Outputs

  • variant_effect_predictions (object) — Predicted effects on gene expression (log TPM), chromatin accessibility, histone marks, splicing, and transcription-factor binding, returned by the hosted AlphaGenome model.

Provenance

Created
Updated
Last verified