agentmods.dev

clinvar-database

clinvar-database is a skill for Claude Code from jimmc414/Kosmos. It costs 45 tokens per session (3,140 once invoked), scanned A, original, no licence file.

A tool for looking up how genetic variants are classified in NCBI ClinVar, a public database of links between DNA changes and health conditions.

In plain words
What is it for?
Use it to search by gene or genomic position, retrieve pathogenicity classifications, access ClinVar data through its API or FTP, and annotate VCF files.
Why use it?
It avoids manually searching variant records and comparing clinical significance labels. It can also provide data for checking variants in VCF files, a common format for genetic test results.

Skill for Claude Code

Written for Claude Code: shipped in a Claude Code plugin.

Part of the scientific-skills plugin — 119 skills shipped together

not rated 605repo +1 28d ago A scan 45 tokens no licence

Good fit Use it to search by gene or genomic position, retrieve pathogenicity classifications, access ClinVar data through its API or FTP, and annotate VCF files.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/jimmc414/kosmos/clinvar-database
View source ↗ jimmc414/Kosmos
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 jimmc414/Kosmos --skill clinvar-database
Clone the repo
git clone --depth 1 https://github.com/jimmc414/Kosmos

Made for: Claude Code.

Or install scientific-skills, the plugin that ships this one along with the rest of its 119 skills.

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 clinvar-database

README.md
[![agentmods](https://agentmods.dev/badge/skills/jimmc414/kosmos/clinvar-database/github.svg)](https://agentmods.dev/skills/jimmc414/kosmos/clinvar-database)
Your own site
<a href="https://agentmods.dev/skills/jimmc414/kosmos/clinvar-database"><img src="https://agentmods.dev/badge/skills/jimmc414/kosmos/clinvar-database/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 clinvar-database

Your own site · 80×15
<a href="https://agentmods.dev/skills/jimmc414/kosmos/clinvar-database"><img src="https://agentmods.dev/badge/skills/jimmc414/kosmos/clinvar-database.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 45 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 3,140 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 1 finding. 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 $0.00045 $0.03140
Opus 5.5 $0.00018 $0.01256
Sonnet 5.5 $0.00009 $0.00628
Haiku 4.5 $0.00005 $0.00314

Measured 2mo ago against content hash de761385bfde, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

clinvar-database scanned grade A with 1 finding 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 2mo 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.

Makes network callslowCapability

Not a fault in itself. Listed so you know the mod talks to something, and to what.

**Quick example using curl:**
kosmos-claude-scientific-skills/scientific-skills/clinvar-database/SKILL.md · 357 lines

The source is not reproduced here

No licence file

A repository with no LICENSE is all rights reserved by default, so the body is not copied here. The metadata, the measurements and the link are.

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. 2mo ago First seen · 357 lines · 45 tokens per session scan A de761385bfde

Subscribe to this mod's changes

clinvar-database is a skill published in the GitHub repository jimmc414/Kosmos (605 stars, last pushed 28d ago), with no licence file. It adds 45 tokens to every session and 3,140 once invoked, about $0.0002 per session on Opus 5.5. A static security scan graded it A with 1 finding (makes network calls). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

ResearchScientific
Related

clinvar-database compared with skills from other repositories

clinvar-database next to 6 skills from other repositories
ModTypeStarsLast pushLicenceScanTokensWorks with
clinvar-databasejimmc414/KosmosSkill60528d agononeA45Claude Code
instrument-data-to-allotropeanthropics/knowledge-work-pluginsSkill35k2d agoApache-2.0A123Claude Code
exploratory-data-analysisK-Dense-AI/scientific-agent-skillsSkill56k4d agoMITA83Claude Code
matlabK-Dense-AI/scientific-agent-skillsSkill56k4d agoMITA44Claude Code
phylogeneticsK-Dense-AI/scientific-agent-skillsSkill56k4d agoMITA71Claude Code, Codex
research-engineerdavila7/claude-code-templatesSkill33kyesterdayMITA43Claude Code, Codex
mapping-to-snomedmaziyarpanahi/openmedSkill5.8kyesterdayApache-2.0A205Claude Code