genomi-gnomad

Research

Fetch reusable public population allele frequencies from gnomAD for a specific variant. Use when the user asks about allele frequency, MAF, population stratification, gnomAD numbers, or rarity of a specific allele.

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How to use this skill

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Prompt to paste

I want to install this Agent Skill for this project in Codex.

Source SKILL.md: https://github.com/exon-research/genomi/blob/HEAD/skills/gnomad/SKILL.md

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Population Frequency (gnomAD)

Fetch public gnomAD population allele frequencies for one variant. Results are cached locally in the evidence database so subsequent queries reuse them.

Activation

To call the tool below, invoke it through the MCP dispatcher:

genomi.invoke({
  "tool": "gnomad.fetch_population_frequency",
  "params": {
    "chrom": "19",
    "pos": 44908684,
    "ref": "T",
    "alt": "C",
    "genome_build": "GRCh38"
  }
})

The dispatcher validates the params against the underlying tool's input schema and returns the underlying tool's response with an added dispatched_tool field.

When to use this skill

"What is the gnomAD frequency of rs429358?"
"Is this variant rare in gnomAD?"
"Allele frequency in African populations for rs1042522."
Any question that needs MAF, AF, population-stratified counts.

Boundaries

Variant-anchored only — query one allele at a time.
Public population data only — does not read the user's Active Genome Index.
Cached after first fetch — subsequent queries for the same variant reuse the local evidence store.

Cross-Capability Synthesis

A scope-limited result from this capability is not a final user-facing answer when other Genomi capabilities can contribute orthogonal evidence to the same question. Returning "cannot answer" while applicable capabilities remain unexamined is a host-agent failure mode.

Tools

gnomad.fetch_population_frequency

Fetch reusable gnomAD public population frequency for one allele and write it into evidence storage.

Use when: The agent needs gnomAD allele frequency, MAF, or population-stratified counts for a specific variant (rsID, chrom/pos/ref/alt, or VCF locus).

Why necessary: gnomAD is the canonical public population frequency source; cached results keep subsequent calls cheap.

Not for: Genome-wide rare-variant screening, ad-hoc curated annotations, anything not anchored to a specific variant.

Example prompts: What's the gnomAD frequency of rs429358? Is rs1042522 rare in East Asian populations?

Result semantics: Returns the gnomAD record with population-stratified counts and frequencies plus a populations block; writes to the local evidence database for reuse.