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 agentmods add skills/exon-research/genomi/clinvarnpx skills add exon-research/genomi --skill clinvargit clone --depth 1 https://github.com/exon-research/genomiWhat 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 | $0.00033 | $0.00892 |
| Opus 5 | $0.00016 | $0.00446 |
| Sonnet 5 | $0.00007 | $0.00178 |
| Haiku 4.5 | $0.00003 | $0.00089 |
Grade A, and why
clinvar scanned grade A with 0 findings 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 yesterday.
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.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 96 lines — stays where its author put it; the contents beside it link to each section on GitHub.
ClinVar Evidence
Use this skill when the user asks about clinical labels, carrier findings, pathogenic/likely pathogenic entries, VUS, conflicting classifications, drug response, risk-factor labels, or ClinVar-derived discovery.
Goal
Build a candidate landscape from exact ClinVar matches. Use
candidate_inventory as variant-level provenance evidence and
candidate_review_groups as the carrier/condition review inventory.
Convention: See
skills/conventions/evidence-quality.md.
Contract
- ClinVar matches provide exact/static evidence for source-backed interpretation.
- Exact matching requires the optional build-specific library
clinvar-grch38orclinvar-grch37. - Candidate inventories are variant-level evidence, not interpretation.
- Candidate review groups are review targets. A heterozygous P/LP group can be carrier-relevance evidence; it is not a carrier-status conclusion.
clinvar.scan_candidatesreturns an evidence view, grouped support, warnings, and coverage; use those fields rather than inferring priority from prose.- By default,
clinvar.scan_candidatesincludes P/LP, conflicting, VUS, risk/association/protective, drug-response, and benign ClinVar groups. - If ClinVar matches are missing,
clinvar.scan_candidatesmaterializes them from the Active Genome Index before building the candidate inventory. - VUS, conflicts, and low-review assertions are downgraded unless reviewed source evidence supports a stronger claim.
- Drug-response rows use pharmacogenomic source context before actionability is implied.
Cross-Capability Synthesis
A scope-limited result from this capability is not a final user-facing answer when other Genomi capabilities can contribute orthogonal evidence to the same question. Returning "cannot answer" while applicable capabilities remain unexamined is a host-agent failure mode.
Tools
clinvar.match_variants
Materialize exact ClinVar matches for comparable Active Genome Index variants using the installed build-specific ClinVar library.
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.
- yesterday First seen · 96 lines · 33 tokens per session scan A 9cc6239a7bda
clinvar is a skill published in the GitHub repository exon-research/genomi (481 stars, last pushed 3d ago), licensed Apache-2.0. It adds 33 tokens to every session and 892 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
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