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Genomics

Interpret genomic variants with ACMG classification, pharmacogenomics, and clinical annotation from ClinVar and gnomAD.

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High Signal

Interpret genomic variants with ACMG classification, pharmacogenomics, and clinical annotation from ClinVar and gnomAD.

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Install for OpenClaw

Quick setup

Download the package from Yavira.
Extract the archive and review SKILL.md first.
Import or place the package into your OpenClaw setup.

Requirements

Target platform: OpenClaw
Install method: Manual import
Extraction: Extract archive
Prerequisites: OpenClaw
Primary doc: SKILL.md

Package facts

Download mode: Yavira redirect
Package format: ZIP package
Source platform: Tencent SkillHub
What's included: SKILL.md, memory-template.md, setup.md

Validation

Use the Yavira download entry.
Review SKILL.md after the package is downloaded.
Confirm the extracted package contains the expected setup assets.

Install with your agent

Agent handoff

Hand the extracted package to your coding agent with a concrete install brief instead of figuring it out manually.

Download the package from Yavira.
Extract it into a folder your agent can access.
Paste one of the prompts below and point your agent at the extracted folder.

New install

I downloaded a skill package from Yavira. Read SKILL.md from the extracted folder and install it by following the included instructions. Tell me what you changed and call out any manual steps you could not complete.

Upgrade existing

I downloaded an updated skill package from Yavira. Read SKILL.md from the extracted folder, compare it with my current installation, and upgrade it while preserving any custom configuration unless the package docs explicitly say otherwise. Summarize what changed and any follow-up checks I should run.

Open Send to Agent page Open JSON manifest Open Markdown brief

Trust & source

Release facts

Source: Tencent SkillHub
Verification: Indexed source record
Version: 1.0.0

Provenance

Publisher: ivangdavila
Source page: View original listing
Canonical URL: Open canonical page

Documentation

ClawHub primary doc Primary doc: SKILL.md 18 sections Open source page

Setup

On first use, read setup.md for integration guidelines. Ask user consent before creating ~/genomics/ workspace.

When to Use

User has processed genomic data (VCF files) and needs clinical interpretation. Agent handles variant classification, pharmacogenomics recommendations, and annotation lookup. NOT for raw data processing — use bioinformatics skill for alignment and variant calling.

Architecture

Memory lives in ~/genomics/. See memory-template.md for structure. ~/genomics/ ├── memory.md # Context + preferences + interpretation history └── cases/ # Active interpretation cases

Quick Reference

TopicFileSetup processsetup.mdMemory templatememory-template.md

1. Classify Variants Using ACMG Guidelines

Every variant needs systematic classification: CategoryCriteriaPathogenicPVS1, PS1-4, PM1-6, PP1-5 weightedLikely PathogenicStrong + moderate evidenceVUSInsufficient or conflicting evidenceLikely BenignBS1-4, BP1-7 weightedBenignStrong benign evidence Never classify without evidence. State "insufficient data" when appropriate.

2. Check Population Frequency First

Before clinical interpretation, verify frequency: SourceUse ForgnomAD v4Global population frequencygnomAD non-cancerSomatic analysisPopulation-specificAncestry-appropriate filtering MAF >1% in any population = likely benign for rare disease.

3. Cross-Reference Multiple Databases

DatabaseInformationClinVarClinical classifications + submitter evidenceOMIMGene-disease relationshipsHGMDLiterature-reported mutationsUniProtProtein function + domains Single-source interpretation is insufficient. Triangulate evidence.

4. Report Pharmacogenomics Actionably

For drug-gene interactions, provide: Diplotype (e.g., CYP2D6 *1/*4) Predicted phenotype (poor/intermediate/normal/ultra-rapid metabolizer) Drug list affected Dosing guidance (CPIC/DPWG when available)

5. Separate Germline from Somatic Context

ContextKey DifferencesGermlineFamily implications, carrier testing, predictiveSomaticTumor-specific, therapy selection, no inheritance Always state which context you're interpreting.

6. Acknowledge Uncertainty

Novel variants often lack evidence VUS ≠ benign — requires ongoing monitoring Reclassification happens (ClinVar updates monthly) Computational predictions are supportive, not definitive

High-Priority Drug-Gene Pairs (CPIC Level A)

GeneDrugsClinical ActionCYP2D6Codeine, tramadol, tamoxifen, SSRIsDosing/alternativeCYP2C19Clopidogrel, PPIs, voriconazoleDosing/alternativeCYP2C9 + VKORC1WarfarinDosing algorithmDPYDFluorouracil, capecitabineDose reduction/avoidTPMT + NUDT15Azathioprine, mercaptopurineDose reductionHLA-B*57:01AbacavirContraindicationHLA-B*15:02CarbamazepineContraindication (Asian ancestry)SLCO1B1SimvastatinDose cap/alternative statinG6PDRasburicase, primaquineContraindicationCYP3A5TacrolimusDosing adjustment

Phenotype Interpretation

Metabolizer StatusMeaningTypical ActionPoor (PM)Little/no enzyme activityAlternative drug or dose ↓↓Intermediate (IM)Reduced activityConsider dose ↓Normal (NM)Expected activityStandard dosingRapid/Ultra-rapid (UM)Increased activityDose ↑ or alternative

Annotation Resources

ResourceURLContentClinVarncbi.nlm.nih.gov/clinvarClinical variant classificationsgnomADgnomad.broadinstitute.orgPopulation frequenciesOMIMomim.orgGene-disease relationshipsPharmGKBpharmgkb.orgDrug-gene annotationsCPICcpicpgx.orgPharmacogenomics guidelinesClinGenclinicalgenome.orgGene-disease validityFranklinfranklin.genoox.comVariant interpretation aidVarSomevarsome.comACMG auto-classification

Common Interpretation Traps

Ignoring population specificity — Variants common in African populations may look rare in European-biased databases Trusting single ClinVar submitter — Check submitter count and review status (≥2 submitters, no conflict preferred) Conflating computational prediction with evidence — CADD/REVEL are supportive, not diagnostic Missing compound heterozygosity — Two VUS in trans can be pathogenic together Outdated database versions — gnomAD v4 has 800K+ exomes vs v2's 125K Ignoring gene-level constraint — pLI/LOEUF scores indicate tolerance to loss-of-function

External Endpoints

This skill does NOT automatically call external APIs. All database references are for manual lookup: ResourceWhen UsedData SentClinVar, gnomAD, OMIMUser manually visitsNone by this skillPharmGKB, CPICUser manually visitsNone by this skillVarSome, FranklinUser manually visitsNone by this skill No automatic network requests. The skill provides URLs and guidance for manual lookup only.

Security & Privacy

Data that stays local: All interpretation work runs locally No variant data sent externally by this skill No automatic API calls to any database This skill does NOT: Make network requests automatically Upload patient variants anywhere Connect to databases without explicit user action Store identifiable genomic information outside ~/genomics/

Related Skills

Install with clawhub install <slug> if user confirms: medicine — clinical decision support biology — molecular mechanisms chemistry — drug metabolism pathways health — patient care context

Feedback

If useful: clawhub star genomics Stay updated: clawhub sync

Category context

Code helpers, APIs, CLIs, browser automation, testing, and developer operations.

Source: Tencent SkillHub

Largest current source with strong distribution and engagement signals.

Package contents

Included in package

3 Docs

SKILL.md Primary doc
memory-template.md Docs
setup.md Docs