clinvar-annotation skillA
clinvar-annotation is agent-read markdown (skill) from ammawla/encode-toolkit: 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..
Indexed from public GitHub and served as immutable, content-addressed versions. Install it pinned to an exact SHA-256 with the mdr CLI, and every file is verified against the hash recorded here before it reaches your agent. The deterministic audit below grades the latest version, and the same file always earns 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@git:20260312.665e731mdr add ammawla/encode-toolkit/clinvar-annotation@sha256:fb7b9f64392f56d2Pin to a label to follow the author's releases, or to a sha256 to freeze the exact bytes forever. Either way the resolved hash is written to mdr.lock, and mdr install reproduces it on any machine.
[](https://markdownregistry.com/a/art_az3onsfbbrald26i)
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Versions
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 (20237 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 · 20 stars · license AGPL-3.0 · pushed 2026-09-21 · 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/fb7b9f64392f56d2b28905263e3b0b995029eb4371314d78f4a762b7a04659cd
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