What is bio-clinical-databases-gnomad-frequencies?

A workflow for querying gnomAD, a large public database of genetic variation in people from the general population, and interpreting gene constraint metrics.

Use it to retrieve allele frequencies, rare-variant frequency limits, gene intolerance scores, and frequency data for structural variants, copy-number variants, or mitochondrial DNA.

It helps distinguish common variants from rare ones and provides population evidence when assessing whether a variant may be medically important.

bio-clinical-databases-gnomad-frequencies — Skill for Claude Code and

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent

npx skills add GPTomics/bioSkills --skill gnomad-frequencies

Clone the repo

git clone --depth 1 https://github.com/GPTomics/bioSkills

Made for: Claude Code, Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/skills/gptomics/bioskills/gnomad-frequencies/github.svg)](https://agentmods.dev/skills/gptomics/bioskills/gnomad-frequencies)

Your own site

<a href="https://agentmods.dev/skills/gptomics/bioskills/gnomad-frequencies"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/gnomad-frequencies/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/skills/gptomics/bioskills/gnomad-frequencies"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/gnomad-frequencies.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 123 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 6,938 The whole file, excluding the scripts and references it only reads on demand.

Security scan B 2 findings. A grade says what 26 rules found in the file — not that it is safe.

Origin original No closer match found in the catalogue.

Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

Model	Per session	Once invoked
Fable 5.1	$0.00123	$0.06938
Opus 5	$0.00062	$0.03469
Sonnet 5	$0.00025	$0.01388
Haiku 4.5	$0.00012	$0.00694

Measured 7d ago against content hash d4435a1e4ba4, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-10, from the pricing page.

Security

Grade B, and why

bio-clinical-databases-gnomad-frequencies scanned grade B with 2 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 7d ago.

The scan reads SKILL.md. This mod also ships 1 executable file (examples/gnomad_query.py), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Sends data to an external URLmediumData exfiltration

A POST to an outside endpoint may be telemetry or may be exfiltration; either way the mod talks to somewhere, and you should know where.

- Python (single variant): GraphQL via `requests.post('https://gnomad.broadinstitute.org/api', json={'query': ..., 'variables': ...})`

Makes network callslowCapability

Not a fault in itself. Listed so you know the mod talks to something, and to what.

- Python (single variant): GraphQL via `requests.post('https://gnomad.broadinstitute.org/api', json={'query': ..., 'variables': ...})`

Origin

Copies of this mod

1 near-identical copy found in the catalogue:

bio-clinical-databases-gnomad-frequencies — 98% identical, 12 lines differ

clinical-databases/gnomad-frequencies/SKILL.md · 423 lines

How it starts

The opening of the file, as written. The whole thing — 423 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Version Compatibility

Reference examples tested with: requests 2.31+, hail 0.2.130+, pandas 2.2+, myvariant 1.0+. Current gnomAD release is v4.1 (May 2024); v4.1 fixed the v4.0 AN under-counting issue that inflated rare-variant AF estimates by 5-10%.

Before using code patterns, verify installed versions match. If versions differ:

Python: pip show <package> then help(module.function) to check signatures
Hail: hl.version(); pin to >=0.2.130 for v4 schema

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. The gnomAD browser GraphQL API at https://gnomad.broadinstitute.org/api is the supported public endpoint; Hail Tables on Google Cloud Storage at gs://gcp-public-data--gnomad/ are the supported bulk access.

gnomAD Frequency Queries and Constraint

'How rare is this variant in the general population?' -> Pull allele frequency, grpmax FAF95 (the ACMG-grade frequency), LOEUF gene-level constraint, structural variant catalog, mtDNA frequencies, and the appropriate dataset version per use case.

Python (single variant): GraphQL via requests.post('https://gnomad.broadinstitute.org/api', json={'query': ..., 'variables': ...})
Python (aggregator): myvariant.MyVariantInfo().getvariant(hgvs, fields=['gnomad_exome', 'gnomad_genome'])
Python (bulk): hl.read_table('gs://gcp-public-data--gnomad/release/4.1/ht/exomes/gnomad.exomes.v4.1.sites.ht')

v2.1.1 / v3.1.2 / v4.x: When to Use Which

This is the most consequential decision in any gnomAD query. The releases are not interchangeable; choice determines what can and cannot be said about a variant.

Release	Build	Samples	Use when	Fails when
v2.1.1	GRCh37	125,748 exomes + 15,708 genomes	Constraint metrics needed (LOEUF v2 most-validated); chrX/Y constraint required; GRCh37 native non-negotiable	GRCh38 native cohort; modern rare-variant FAF95 (use v4)
v3.1.2	GRCh38	76,156 genomes (NO exomes)	Non-coding region rare variants on GRCh38; mtDNA frequencies	Exome variants needed (no exomes); 76k cohort smaller than v4
v4.0/v4.1	GRCh38	730,947 exomes + 76,215 genomes = 807,162 total	Default for everything; rare-variant filtering, FAF95, gene queries	chrX/Y constraint (not released); cancer-cohort analysis (no TCGA in v4)

Read the full file on GitHub · 423 lines

Files

What ships with it

2 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

7d ago First seen · 423 lines · 123 tokens per session scan B d4435a1e4ba4

Subscribe to this mod's changes

bio-clinical-databases-gnomad-frequencies is a skill published in the GitHub repository GPTomics/bioSkills (1,199 stars, last pushed 26d ago), licensed MIT. It adds 123 tokens to every session and 6,938 once invoked, about $0.0006 per session on Opus 5. A static security scan graded it B with 2 findings (sends data to an external url, makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.

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bio-clinical-databases-gnomad-frequencies