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Clinvar Database

Listed
jimmc414·vlatest·database

Queries ClinVar to retrieve genetic variant information, including classifications, interpretations, and associated publications.

Repository

Install on your platform

Showing Claude Code. One command installs this skill into any of the agents below.

  1. 1

    Run this in your project

    terminal
    $ npx skills add jimmc414/kosmos --skill clinvar-database -a claude-code

  2. Uses the open-source skills CLI and needs Node.js. Add -g to install it for your user instead of this project.

What we know about this skill

Publisher

jimmc414

Taken from the source listing. We haven't verified who controls this account.

Install target

Live repository

Not pinned. Installing fetches whatever the repository holds at the time you run the command.

No human has reviewed this code. The checks below are a static scan of the files at one commit — nobody has run this skill or judged whether it works. A skill runs with whatever access you give your agent, so read the source before you install it.

Automated safety checks

scanned

This skill failed 2 of 6 checks. A failure is not proof of bad intent; it means something in the code needs a human to look at it before you run it.

  • No undeclared network calls: failed

    Contacts 2 hosts that are neither well-known infrastructure nor declared in the skill's frontmatter: eutils.ncbi.nlm.nih.gov, ftp.ncbi.nlm.nih.gov.

    Every host the skill dials — from its scripts, its config endpoints or the commands it tells the agent to run — is either well-known package and API infrastructure or declared in its own frontmatter. Links in documentation are not counted.

    Hosts contacted

    eutils.ncbi.nlm.nih.govundeclaredftp.ncbi.nlm.nih.govundeclared

    What it found (3 of 11)

    • kosmos-claude-scientific-skills/scientific-skills/clinvar-database/SKILL.md:51contacts eutils.ncbi.nlm.nih.gov
      curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=clinvar&term=BRCA1[gene]+AND+pathogenic[CLNSIG]&retmode=json"
    • kosmos-claude-scientific-skills/scientific-skills/clinvar-database/references/api_reference.md:38contacts eutils.ncbi.nlm.nih.gov
      curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=clinvar&term=BRCA1[gene]+AND+pathogenic[CLNSIG]&retmode=json&retmax=100"
    • kosmos-claude-scientific-skills/scientific-skills/clinvar-database/references/api_reference.md:66contacts eutils.ncbi.nlm.nih.gov
      curl "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=clinvar&id=12345&retmode=json&version=2.0"

  • No pipe-to-shell installers: failed

    Runs code fetched at install time in 1 place.

    No `curl … | sh` pattern, in the code or in the instructions, that runs code fetched at run time.

    What it found

    • kosmos-claude-scientific-skills/scientific-skills/clinvar-database/references/api_reference.md:138remote script run via command substitution
      sh -c "$(curl -fsSL ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/install-edirect.sh)"

  • Declares what it does: passed

    SKILL.md parses and declares a name and a description.

    SKILL.md exists, its frontmatter parses, and it declares a name and a description.

  • No obfuscated payloads: passed

    No encoded or obfuscated payloads.

    No base64, hex or compressed blob is decoded and then executed, and no encoded shell commands.

  • No credential access: passed

    Reads no keys, tokens, keychains or credential files.

    Neither the code nor the SKILL.md instructions read SSH keys, cloud credentials, keychains, token stores, browser cookie databases or dotfiles that hold secrets.

  • Pinned to a commit: passed

    Scanned jimmc414/kosmos at 6cfe7f690d.

    The exact upstream commit SHA that was scanned is recorded, so the result refers to specific bytes.

Commit
6cfe7f690d
Manifest
kosmos-claude-scientific-skills/scientific-skills/clinvar-database/SKILL.md
Scanned
4 files, 1,073 lines
This is a static scan, not a review. It reads the skill's files; it does not run them, and it cannot tell you whether the skill is any good or whether the code does what its description says. A skill runs with whatever access you give your agent.
What each check looks for →

About this skill

What it does

This skill provides access to and querying capabilities of the ClinVar database, a public archive of reports of relationships among human genes, genetic variants, and phenotypes (observable characteristics). It allows users to retrieve variant information including clinical significance classifications, associated diseases, and submission details. The skill facilitates research into genetic disorders and personalized medicine applications by enabling programmatic access to this valuable resource.

When to use it

  • Investigating the clinical significance of a specific gene variant.
  • Identifying genes or variants associated with a particular disease phenotype.
  • Analyzing trends in variant reporting and classification over time.
  • Building tools for genetic counseling or personalized medicine applications.
  • Researching the impact of genetic variations on drug response.

Key capabilities

  • Variant querying by gene name, chromosome position, or RefSeq transcript ID.
  • Retrieval of clinical significance classifications (e.g., Pathogenic, Benign).
  • Access to associated diseases and phenotypes.
  • Information about variant submitters and review status.

Example prompts

  • "What is the clinical significance of the BRCA1 c.185delAG variant?"
  • "Find all pathogenic variants in the TP53 gene."
  • "Show me the submission details for rsid 1234567."

Tips & gotchas

The ClinVar database can be complex, and results may require interpretation by a qualified professional. Be aware that variant classifications are subject to change as new evidence emerges.