bio-clinical-databases-gnomad-frequencies SKILL.md skillA
bio-clinical-databases-gnomad-frequencies from pku-yuangroup/openai4s is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add pku-yuangroup/openai4s/bio-clinical-databases-gnomad-frequencies@git:20260821.2d1b678Pins git:20260821.2d1b678 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- pku-yuangroup/openai4s
- Path
skills/bioskills/bio-clinical-databases-gnomad-frequencies/SKILL.md- Versions recorded
- 1
- Latest version
- git:20260821.2d1b678, committed Aug 21, 2026
- Size
- 25,050 bytes
- Repository stars
- 662
- License
- MIT
Queries gnomAD v4 (807k samples), v3, v2.1.1, and constraint metrics with grpmax FAF95, bottleneck-group exclusion, LOEUF interpretation, SV/CNV/mtDNA catalogs, and Whiffin max-credible-AF framework. Use when filtering rare variants, applying ACMG BS1/BA1, ranking genes by LoF intolerance, or selecting between v2 (GRCh37 + chrX/Y constraint) and v4 (GRCh38 + 807k samples).
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
## 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. …
Read the whole file at its exact version.
How to install
mdr add pku-yuangroup/openai4s/bio-clinical-databases-gnomad-frequencies@sha256:d753f1b457b23e3aThe line at the top of this page pins the label git:20260821.2d1b678, 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.
[](https://markdownregistry.com/a/art_ginnoyb2mlu6jhb7)
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Versions
The registry has recorded 1 version of this file, committed on Aug 21, 2026.
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Source
pku-yuangroup/openai4s · 662 stars · license MIT · pushed 2026-11-03 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_ginnoyb2mlu6jhb7 GET https://markdownregistry.com/api/v1/resolve?ref=pku-yuangroup/openai4s/bio-clinical-databases-gnomad-frequencies GET https://markdownregistry.com/api/v1/blob/d753f1b457b23e3ae1b2b2715ce41e5c88e4f5bf8b888468a8e44ed071f1c5d9
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