clinvar-annotation SKILL.md skillA
clinvar-annotation from ammawla/encode-toolkit is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add ammawla/encode-toolkit/clinvar-annotation@git:20260920.6050003Pins 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/clinvar-annotation/SKILL.md- Versions recorded
- 3
- Latest version
- git:20260920.6050003, committed Sep 20, 2026
- First version recorded
- Mar 12, 2026
- Size
- 20,793 bytes
- Repository stars
- 21
- License
- AGPL-3.0
Guide for annotating ENCODE regulatory variants with ClinVar clinical significance. Use when users need to check if variants in ENCODE peaks have clinical associations, find pathogenic variants in regulatory regions, or assess variant clinical impact. Trigger on: ClinVar, clinical significance, pathogenic variant, variant classification, clinical variant, disease variant, VUS, benign, likely pathogenic.
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
## When to Use - User wants to check if variants in ENCODE regulatory peaks have clinical significance in ClinVar - User asks about "ClinVar", "pathogenic variants", "clinical significance", or "variant classification" - User needs to annotate ENCODE-derived regulatory variants with disease associations - User wants to find clinically relevant variants within enhancers, promoters, or open chromatin regions - Example queries: "check ClinVar for variants in my ATAC-seq peaks", "find pathogenic variants in pancreas enhancers", "annotate regulatory variants with clinical significance" # Annotating ENCODE Regulatory Variants with ClinVar Clinical Significance Cross-reference ENCODE functional genomic elements with ClinVar clinical variant classifications to identify pathogenic variants in regulatory regions and understand non-coding disease mechanisms. ## Scientific Rationale **The question**: "Do any clinically significant variants fall within my ENCODE regulatory elements, and can ENCODE data explain their pathogenic mechanism?" …
Read the whole file at its exact version.
How to install
mdr add ammawla/encode-toolkit/clinvar-annotation@sha256:4ceac52ed8ec52caThe 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.
[](https://markdownregistry.com/a/art_az3onsfbbrald26i)
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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 | 20,793 B | A | view · diff |
| git:20260920.ce7840d | 2026-09-20 | ce7840d | 20,227 B | A | view · diff |
| git:20260312.665e731 | 2026-03-12 | 665e731 | 20,237 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (20793 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
ammawla/encode-toolkit · 21 stars · license AGPL-3.0 · pushed 2026-09-27 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_az3onsfbbrald26i GET https://markdownregistry.com/api/v1/resolve?ref=ammawla/encode-toolkit/clinvar-annotation GET https://markdownregistry.com/api/v1/blob/4ceac52ed8ec52ca92556ae2d0759f644cf9eee004e16f8d20e5650455a6c2b3
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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