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.
npx skills add AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-clinvargit clone --depth 1 https://github.com/AlterLab-IEU/AlterLab-Academic-SkillsWrote 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.
[](https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-clinvar)<a href="https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-clinvar"><img src="https://agentmods.dev/badge/skills/alterlab-ieu/alterlab-academic-skills/alterlab-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.
<a href="https://agentmods.dev/skills/alterlab-ieu/alterlab-academic-skills/alterlab-clinvar"><img src="https://agentmods.dev/badge/skills/alterlab-ieu/alterlab-academic-skills/alterlab-clinvar.svg" alt="Reviewed on agentmods" width="80" height="20"></a>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 | $0.00133 | $0.04296 |
| Opus 5.5 | $0.00053 | $0.01718 |
| Sonnet 5.5 | $0.00027 | $0.00859 |
| Haiku 4.5 | $0.00013 | $0.00430 |
Grade A, and why
alterlab-clinvar 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 1mo 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.
allowed-tools: Read WebFetch Bash(curl:*) Bash(python:*) This is a copy
88% identical to clinvar-database — 137 lines differ, which has more behind it and is treated as the original. This page carries a canonical link to it rather than competing with it.
How it starts
The opening of the file, as written. The whole thing — 405 lines — stays where its author put it; the contents beside it link to each section on GitHub.
ClinVar Database
Overview
ClinVar is NCBI's freely accessible archive of reports on relationships between human genetic variants and phenotypes, with supporting evidence. The database aggregates information about genomic variation and its relationship to human health, providing standardized variant classifications used in clinical genetics and research.
When to Use This Skill
This skill should be used when:
- Searching for variants by gene, condition, or clinical significance
- Interpreting clinical significance classifications (pathogenic, benign, VUS)
- Accessing ClinVar data programmatically via E-utilities API
- Downloading and processing bulk data from FTP
- Understanding review status and star ratings
- Resolving conflicting variant interpretations
- Annotating variant call sets with clinical significance
Does NOT Trigger
| Scenario | Use Instead |
|---|---|
| Population allele frequency / ancestry-specific AF, gnomAD constraint | alterlab-gnomad |
| Somatic cancer mutation catalog, Cancer Gene Census, mutational signatures | alterlab-cosmic |
| How often a gene is mutated in tumor cohorts (TCGA, MSK-IMPACT) | alterlab-cbioportal |
| Pharmacogenomic gene–drug dosing (CPIC/DPWG) | alterlab-clinpgx |
Three classification types (since 2024). ClinVar now keeps separate aggregate
classifications for germline pathogenicity (ACMG/AMP), somatic clinical impact
(AMP/ASCO/CAP tiers), and oncogenicity (ClinGen/CGC/VICC). APIs and files expose them
separately: esummary JSON has germline_classification, clinical_impact_classification,
and oncogenicity_classification objects (each with description and review_status;
there is no longer a clinical_significance field); the VCF has CLNSIG/CLNREVSTAT
(germline), ONC/ONCREVSTAT, and SCI/SCIREVSTAT; variant_summary.txt has
ClinicalSignificance (germline) plus SomaticClinicalImpact and Oncogenicity columns.
Core Capabilities
1. Search and Query ClinVar
What ships with it
5 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.
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.
- 1mo ago Changed · +28 lines ce0f0bf6a011
- 1mo ago First seen · 377 lines · 133 tokens per session scan A e2ea5b793f13
alterlab-clinvar is a skill published in the GitHub repository AlterLab-IEU/AlterLab-Academic-Skills (78 stars, last pushed 2d ago), licensed MIT. It adds 133 tokens to every session and 4,296 once invoked, about $0.0005 per session on Opus 5.5. A static security scan graded it A with 1 finding (makes network calls). It is 88% identical to clinvar-database, differing in 137 lines, and is treated as a copy.
Other skills, from other repositories
r-spss-syntax-architect
A guide for turning research hypotheses into repeatable R or SPSS code for statistical analysis. It covers panel data, where the same companies or other units are observed over time, as well as interaction effects, curves, and mediation.
management-figure
A chart-making toolkit for evidence-based management, finance, and strategy research. It creates publication-ready plots from regression results and tracking data, including coefficient, interaction, group-comparison, trend, and curved-relationship charts.
ob-hrm-scale-adaptor
A guide for adapting organisational behaviour and human-resources survey scales across languages and cultures. It covers permission checks, translation and back-translation, expert review, participant interviews, and tests of whether groups interpret the scale comparably.
thesis-consistency-audit
A consistency audit for quantitative master’s and doctoral theses in management, finance, or strategy. It checks whether numbers, tables, analyses, and claims agree, and can inspect hidden author information in office documents.
reproducibility-architect
A guide for packaging research so another person can rerun its data processing and analysis. A replication package is the project files, instructions, code, data guidance, and software details needed to reproduce published results.
journal-submission-scout
A research tool for choosing a journal for a completed paper. It searches for journals that publish similar work, compares public information such as citation data, fees, open-access listing, and review practices, and screens for warning signs of predatory journals, which charge authors without providing trustworthy publishing services.