ncbi_clinvar

ncbi_clinvar is a skill for Claude Code, Codex from ai4protein/VenusFactory2. It costs 53 tokens per session (2,361 once invoked), scanned A, original, no licence file.

A guide for querying ClinVar, an NCBI database that collects reports about how genetic variants relate to disease. It can search variants by gene, condition, or clinical-significance label and annotate VCF files.

In plain words
What is it for?
Use it to search variant records, examine reported pathogenicity, filter by clinical significance, or add ClinVar annotations to VCF variant files.
Why use it?
It helps organize existing clinical evidence about variants and their reported importance instead of interpreting each variant from scratch.

Skill for Claude CodeCodex

Which agent this was written for is unclear — body not stored (licence); the path alone says nothing.

Good fit Use it to search variant records, examine reported pathogenicity, filter by clinical significance, or add ClinVar annotations to VCF variant files.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/ai4protein/venusfactory2/ncbi_clinvar
Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent
npx skills add ai4protein/VenusFactory2 --skill ncbi_clinvar
Clone the repo
git clone --depth 1 https://github.com/ai4protein/VenusFactory2

Made for: Claude Code, Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for ncbi_clinvar

README.md
[![agentmods](https://agentmods.dev/badge/skills/ai4protein/venusfactory2/ncbi_clinvar/github.svg)](https://agentmods.dev/skills/ai4protein/venusfactory2/ncbi_clinvar)
Your own site
<a href="https://agentmods.dev/skills/ai4protein/venusfactory2/ncbi_clinvar"><img src="https://agentmods.dev/badge/skills/ai4protein/venusfactory2/ncbi_clinvar/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for ncbi_clinvar

Your own site · 80×15
<a href="https://agentmods.dev/skills/ai4protein/venusfactory2/ncbi_clinvar"><img src="https://agentmods.dev/badge/skills/ai4protein/venusfactory2/ncbi_clinvar.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 53 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 2,361 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin unknown No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00053 $0.02361
Opus 5 $0.00026 $0.01180
Sonnet 5 $0.00011 $0.00472
Haiku 4.5 $0.00005 $0.00236

Measured 11d ago against content hash a58eeaa0a614, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-10, from the pricing page.

Security

Grade A, and why

ncbi_clinvar scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 11d ago.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

src/agent/skills/ncbi_clinvar/SKILL.md · 174 lines

The source is not reproduced here

A licence we could not identify

The repository carries a LICENSE file, but it is custom or dual enough that GitHub cannot name it and neither can this catalogue. Unknown terms are not permission, so the body is not copied here. Read the licence at the source and decide for yourself.

Read it on GitHub

Files

What ships with it

3 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 11d ago First seen · 174 lines · 53 tokens per session scan A a58eeaa0a614

Subscribe to this mod's changes

ncbi_clinvar is a skill published in the GitHub repository ai4protein/VenusFactory2 (248 stars, last pushed 1mo ago), with no licence file. It adds 53 tokens to every session and 2,361 once invoked, about $0.0003 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

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