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gnomAD Database · mkurman | DecimalAI

scienceby mkurman

gnomAD Database

mkurman/gnomad-database

Source mkurman/zorai ↗License MIT

Query the Genome Aggregation Database (gnomAD).

SkillScore50Maintained

Automatic

Research pack

Last verified 8/21/2026

What it changes

Passed 6 of 11 test cases with the skill, and 3 of 11 without it.

Without skill27%

With skill50%

Checks it passed that the model alone missed

Uses region_variants.json as the output filename.
Uses the full path to scripts/get_variant_frequency.py.
Invokes the script using uv run rather than system python.

and 4 more in the full report

6 fixed5 passed either way10 still failing1 broke

Pass-rate lift: +23 pp
Tokens: +9%
Agent turns: 0%
Response time: -31%

Model gemini-3.6-flashMeasured 8/21/2026v111 of 22 cases passed with skill · 11 comparable

Tokens, turns and time describe resource use, not a dollar price.

Use this skill

Save it into your project's skills folder. Claude Code picks it up in its next session.

curl -fsSL --create-dirs -o .claude/skills/mkurman-gnomad-database/SKILL.md https://app.decimal.ai/s/mkurman-gnomad-database/SKILL.md

Want it pinned and updatable? pip install "decimalai>=0.15", then decimalai skills add mkurman-gnomad-database, and start Claude Code with claude --plugin-dir "$(git rev-parse --show-toplevel)/.agents"

1 · One-time — install the CLI (docs ↗)

pip install "decimalai>=0.15"

2 · Get the skill — writes .agents/skills/mkurman-gnomad-database/ and pins it in .decimal/skills.lock

decimalai skills add mkurman-gnomad-database

No CLI? Get the same file — curl · raw file

curl -fsSL --create-dirs -o .claude/skills/mkurman-gnomad-database/SKILL.md https://app.decimal.ai/s/mkurman-gnomad-database/SKILL.md

Raw file: /s/mkurman-gnomad-database/SKILL.md ↗ · machine-readable summary at /s/mkurman-gnomad-database.json ↗

Safety checks: 3 of 3 passed

Code scan CleanIntent PassedContent Clean

See it in action

One of 6 test cases the skill fixed. Same model, same prompt, with and without the skill.

1 of 6

Prompt

When searching for variants across chromosome 12 between positions 100000 and 200000 using search_variants.py, what is the default output filename expected by the helper conventions?

What was checked, without and with the skill
Checked	Without skill	With skill
Uses region_variants.json as the output filename.	Missed	Passed

case-19 · gemini-3.6-flash · 8/21/2026 · answers are capped and redacted

What's inside

The instructions your model reads when the skill loads.

SKILL.md62 lines4 filesincludes scripts

gnomAD Database

Prerequisites

uv: Read the uv skill and follow its Setup instructions to ensure uv is installed and on PATH.
User Notification: If LICENSE_NOTIFICATION.txt does not already exist in this skill directory then (1) prominently notify the user to check the terms at https://gnomad.broadinstitute.org/policies and https://gnomad.broadinstitute.org/data#api, then (2) create the file recording the notification text and timestamp.

Core Rules

Use the Wrapper: ALWAYS execute the provided helper scripts to query the database rather than accessing the database directly. The scripts automatically enforce the gnomAD API rate limits gracefully.
Notification: If this skill is used, ensure this is mentioned in the output.

Utility Scripts

All scripts are located in the scripts/ subdirectory of this skill's installation directory. When running them, use the full absolute path to the script (e.g. /path/to/gnomad_database/scripts/get_variant_frequency.py).

1. Variant Frequency. Retrieves global and ancestry-specific allele frequencies, homozygote counts, and Grpmax Filtering AF (faf95/faf99) for exome, genome, and total (exome+genome combined) data. The filtering allele frequency (FAF) is the maximum credible genetic ancestry group AF (lower bound of the 95% or 99% CI). Variant ID format must be chrom-pos-ref-alt (e.g., 1-55516888-G-GA). Alternately, you may provide an rsID.

# By variant ID:
uv run scripts/get_variant_frequency.py --variant_id {variant_id} [--dataset {dataset}] --output variant_frequency.json

# By rsID (e.g., rs1800562):
uv run scripts/get_variant_frequency.py --rsid {rsid} [--dataset {dataset}] --output variant_frequency.json

Track record

Benchmark

6 / 11

test cases passed, vs 3 / 11 without

Adoption

Users: 0
Times used: 0

Safety and source details

SkillSafety

✓ 3 of 3 passed

Code scan15 of 15 checks clean

0 critical · 0 warning · 0 info — scanner v4 — 8/3/2026

View 15 scanner checks

live_secretremote_code_executionreverse_shelldata_exfiltrationssrf_metadataagent_snoopinganti_refusaldestructive_commandsobfuscated_unicodeunicode_homoglyphopaque_blobsuspicious_urltool_overreachtrigger_abuseprompt_injection_phrasing

IntentSafe

LLM judge · does the skill do what it claims

ContentClean

LLM judge · policy & harmful-content review

Source

Imported

mkurman / zorai

skills/scientific-skills-gdm/gnomad_database/SKILL.md

View on GitHub ↗

License MITImported 8/3/2026Version v1Bundled 3 files · scripts

Other skills for the same job

Published skills whose descriptions closely match this one, with their headline benchmark lift.

gnomad-databaseQuery gnomAD (Genome Aggregation Database) for population allele frequencies, variant constraint scores (pLI, LOEUF), and loss-of-function intolerance. Essential for variant pathogenicity interpretation, rare disease genetics, and identifying loss-of-function intolerant genes.Close match0 pp pass-rate lift

More skills from the same source and nearby in the registry, with their headline benchmark lift.

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See it in action

What's inside

gnomAD Database

Prerequisites

Core Rules

Utility Scripts

Track record

Benchmark

Adoption

SkillSafety

Source

Other skills for the same job

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