What is bio-clinical-databases-clinvar-lookup?

A clinical genetics lookup tool for ClinVar, a public database of genetic variants and their reported medical significance. It retrieves aggregate classifications, individual submissions, expert-panel reviews, and conflict information.

Use it to look up a variant, compare clinical significance classifications, inspect ClinGen expert-panel decisions, and query batches of variants from REST data, VCF files, or XML.

It helps you compare variant interpretations in one place instead of manually checking different ClinVar records and evidence sources. This is useful when reports disagree or when ACMG/AMP evidence must be reviewed.

bio-clinical-databases-clinvar-lookup — Skill for Claude Code and Code

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 GPTomics/bioSkills --skill clinvar-lookup

Clone the repo

git clone --depth 1 https://github.com/GPTomics/bioSkills

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.

README.md

[![agentmods](https://agentmods.dev/badge/skills/gptomics/bioskills/clinvar-lookup/github.svg)](https://agentmods.dev/skills/gptomics/bioskills/clinvar-lookup)

Your own site

<a href="https://agentmods.dev/skills/gptomics/bioskills/clinvar-lookup"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/clinvar-lookup/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.

Your own site · 80×15

<a href="https://agentmods.dev/skills/gptomics/bioskills/clinvar-lookup"><img src="https://agentmods.dev/badge/skills/gptomics/bioskills/clinvar-lookup.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 79 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 5,739 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 original 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.

Model	Per session	Once invoked
Fable 5.1	$0.00079	$0.05739
Opus 5	$0.00039	$0.02870
Sonnet 5	$0.00016	$0.01148
Haiku 4.5	$0.00008	$0.00574

Measured 7d ago against content hash 7479e7d15553, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-10, from the pricing page.

Security

Grade A, and why

bio-clinical-databases-clinvar-lookup 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 7d ago.

The scan reads SKILL.md. This mod also ships 1 executable file (examples/clinvar_query.py), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

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.

- Python (REST): `requests.get()` against the E-utilities `clinvar` database

Origin

Copies of this mod

1 near-identical copy found in the catalogue:

bio-clinical-databases-clinvar-lookup — 100% identical, 12 lines differ

clinical-databases/clinvar-lookup/SKILL.md · 310 lines

How it starts

The opening of the file, as written. The whole thing — 310 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Version Compatibility

Reference examples tested with: requests 2.31+, cyvcf2 0.30+, pandas 2.2+, bcftools 1.19+, Entrez Direct 21.0+, lxml 5.0+ (for v2 XML schema).

Before using code patterns, verify installed versions match. If versions differ:

Python: pip show <package> then help(module.function) to check signatures
CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. ClinVar XML schema v2 (rolled out in 2024) replaces <ClinVarSet> with <VariationArchive> as the top-level anchor; XSLT or parsers targeting the legacy element silently emit zero records.

ClinVar Lookup and Clinical-Significance Triangulation

'Look up the clinical significance of this variant' -> Retrieve ClinVar VCV-level aggregate, SCV-level submissions, ClinGen Variant Curation Expert Panel (VCEP) overrides, and conflict-resolution status.

Python (REST): requests.get() against the E-utilities clinvar database
Python (local VCF): cyvcf2.VCF('clinvar.vcf.gz') for batch queries against the weekly snapshot
CLI: bcftools annotate -a clinvar.vcf.gz -c INFO/CLNSIG,INFO/CLNREVSTAT,INFO/CLNDN
Cross-database: ClinGen Allele Registry CA ID via https://reg.clinicalgenome.org/

The Identifier Hierarchy (VCV / SCV / RCV): Get This Wrong and Everything Downstream Breaks

Level	Format	What it aggregates	When to use	Fails when
SCV	`SCVxxxxxxxxx.N`	One submitter, one variant, one condition (atomic submission unit)	Auditing who said what; conflict triangulation	Aggregated reporting (use VCV); cross-condition analysis
RCV	`RCVxxxxxxxxx.N`	All SCVs for a single (variant, condition) pair	Condition-stratified analysis; legacy aggregation	Variant-level reporting across all conditions (use VCV)
VCV	`VCVxxxxxxxxx.N`	All RCVs for one variant across all conditions	Canonical anchor since 2017; default API entrypoint	Condition-specific clinical action (use RCV); CLNSIG collapses multi-condition

Read the full file on GitHub · 310 lines

Files

What ships with it

2 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.

7d ago First seen · 310 lines · 79 tokens per session scan A 7479e7d15553

Subscribe to this mod's changes

bio-clinical-databases-clinvar-lookup is a skill published in the GitHub repository GPTomics/bioSkills (1,199 stars, last pushed 26d ago), licensed MIT. It adds 79 tokens to every session and 5,739 once invoked, about $0.0004 per session on Opus 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 2026-09-03.

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bio-clinical-databases-clinvar-lookup