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Clinvar Database

Listed
drshailesh88·vlatest·database

Access and query ClinVar data via drshailesh88's agent to retrieve variant information and clinical significance assessments.

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 drshailesh88/integrated_content_os --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

drshailesh88

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)

    • skills/scientific/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"
    • skills/scientific/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"
    • skills/scientific/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

    • skills/scientific/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 drshailesh88/integrated_content_os at 9e61937ad2.

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

Commit
9e61937ad2
Manifest
skills/scientific/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 the ClinVar database, a public archive of reports describing relationships among human genes, genetic variants and phenotypes. It allows users to query this data for specific gene or variant information, including clinical significance classifications and associated publications. The tool can be used to retrieve detailed information about genetic variations and their impact on health.

When to use it

  • Researching the clinical significance of a particular genetic variant.
  • Understanding the reported phenotypes associated with a specific gene.
  • Identifying relevant publications related to a genetic condition or variant.
  • Analyzing data for potential drug targets based on genetic variation impacts.
  • Supporting diagnostic investigations by providing comprehensive variant information.

Key capabilities

  • Querying the ClinVar database.
  • Retrieving clinical significance classifications.
  • Accessing associated publications and reports.
  • Searching by gene or variant name.
  • Providing detailed variant information.

Example prompts

  • "What is the clinical significance of the BRCA1 c.185delAG variant?"
  • "Find all variants associated with Alzheimer's disease in ClinVar."
  • "Show me publications related to mutations in the TP53 gene."
  • "Retrieve information about the CYP2C9 gene and its variants."

Tips & gotchas

The accuracy of results depends on the completeness and quality of data within the ClinVar database. Be aware that clinical significance classifications can change as new evidence emerges.