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gnomad-variants SKILL.md skillA

gnomad-variants from ammawla/encode-toolkit is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.

Install it, pinned

mdr add ammawla/encode-toolkit/gnomad-variants@git:20260920.6050003

Pins git:20260920.6050003 in mdr.lock. Pin the fingerprint instead.

Audit grade: A, 17 of 17 checks passed
Kind: SKILL.md skill
Repository: ammawla/encode-toolkit
Path: plugin/skills/gnomad-variants/SKILL.md
Versions recorded: 3
Latest version: git:20260920.6050003, committed Sep 20, 2026
First version recorded: Mar 12, 2026
Size: 17,198 bytes
Repository stars: 21
License: AGPL-3.0

Query gnomAD (Genome Aggregation Database) for population allele frequencies, gene constraint scores, and variant annotations to interpret ENCODE regulatory variants. Use when the user needs allele frequencies for variants in ENCODE regulatory elements, wants to assess gene constraint (pLI, LOEUF) for ENCODE target genes, needs population-specific frequencies for GWAS variants overlapping cCREs, wants to filter variants by rarity before functional annotation, or is interpreting ENCODE…

Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.

What the file says

# Query gnomAD for Population Variant Data

## When to Use

- User wants to check population allele frequencies for variants in ENCODE regulatory regions
- User asks about "gnomAD", "allele frequency", "population genetics", "gene constraint", or "variant frequency"
- User needs to filter regulatory variants by rarity (common vs rare) using population data
- User wants to assess gene constraint (pLI, LOEUF) for targets identified from ENCODE ChIP-seq
- Example queries: "check gnomAD frequency for variants in my peaks", "is this regulatory variant rare?", "what's the constraint score for CTCF?"

Annotate ENCODE-identified regulatory variants with population allele frequencies and gene constraint scores from the Genome Aggregation Database.

## Scientific Rationale

**The question**: "How common is this variant in the population, and how constrained is the gene it regulates?"
…

Read the whole file at its exact version.

How to install

The exact contents, by fingerprint

mdr add ammawla/encode-toolkit/gnomad-variants@sha256:cee9158a457f52ca

The line at the top of this page pins the label git:20260920.6050003, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.

Badge

[![mdr](https://markdownregistry.com/badge/art_gdbwpcew5sdmwzzk.svg)](https://markdownregistry.com/a/art_gdbwpcew5sdmwzzk)

3 badge image fetches in 30 days. What the badge shows.

Versions

The registry has recorded 3 versions of this file, between Mar 12, 2026 and Sep 20, 2026, about one every 96 days.

version	committed	commit	size	audit
git:20260920.6050003 latest	2026-09-20	6050003	17,198 B	A	view · diff
git:20260920.ce7840d	2026-09-20	ce7840d	16,631 B	A	view · diff
git:20260312.665e731	2026-03-12	665e731	16,641 B	A	view

Audit of the latest version

A 17 of 17 checks passed. Fixed automatic checks with no AI involved, so the same checks give the same answer every run.

pass: Frontmatter block present
pass: Frontmatter declares a name
pass: Frontmatter declares a description
pass: Size between 200 bytes and 200 KB (17198 bytes)
pass: No zero-width or bidi control characters
pass: No instruction hidden inside an HTML comment
pass: No link to an exfiltration or paste host
pass: No credential-shaped string
pass: No instruction to send local credentials anywhere
pass: No text hidden with inline styles
pass: No prompt-injection phrasing
pass: No curl or wget piped into a shell
pass: No recursive delete of root, home or parent
pass: No instruction to read or print local credentials
pass: No base64 blob over 200 characters
pass: No link to a raw IP address
pass: No script tag

Source

GitHub

ammawla/encode-toolkit · 21 stars · license AGPL-3.0 · pushed 2026-09-27 · branch main

API

GET https://markdownregistry.com/api/v1/artifacts/art_gdbwpcew5sdmwzzk
GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/gnomad-variants
GET https://markdownregistry.com/api/v1/blob/cee9158a457f52ca41b3c5310ba550e4d43a155387a2fa83d044b1de5b318671

Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.

Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.

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