gnomad-search

name	gnomad-search
description	Query gnomAD for variant allele frequency/rarity, gene constraint metrics (pLI, LOEUF), variants in a region or gene, and structural variants. Use to assess variant rarity or loss-of-function intolerance. Not for individual patient genomes or somatic cancer variants. Public GraphQL API, no credential needed.
license	Apache-2.0

Gnomad Search (Codex-native)

Codex-native adaptation of Google DeepMind's gnomad-database skill (science-skills, Apache-2.0). Uses the public API directly through Codex's own tools.

Gates (ask before proceeding)

• Terms notice: on first use in a workspace, tell the user to review the source's terms of use and record the notice in provenance.
• Network / install: read-only public access; be polite about rate limits. Write large responses to a file and parse them; if you write helper code, run it via uv run, never bare python3. Ask before installs or large downloads.

Endpoints

• gnomAD GraphQL https://gnomad.broadinstitute.org/api

Workflow

1. POST a GraphQL query for a variant (by ID/rsID), a gene, or a region; request the gnomAD version/dataset explicitly.
2. For constraint, request gnomad_constraint fields (pLI, LOEUF, oe) on the gene.

• Provenance & review: record queries, endpoints, and cited identifiers with $science-provenance; check claims with $science-review before presenting.

Boundaries

• Report the gnomAD dataset version and population; allele frequency is population-dependent.
• Population frequency is not clinical classification; cite only variants actually returned.