Clinical Variant Interpreter

Systematic variant interpretation using ToolUniverse - from raw variant calls to ACMG-classified clinical recommendations with structural impact analysis.

Triggers

Use this skill when users:

Ask about variant interpretation, classification, or pathogenicity

Have VCF data needing clinical annotation

Need ACMG classification for variants

Want structural impact analysis for missense variants

Key Principles

ACMG-Guided

- Follow ACMG/AMP 2015 guidelines with explicit evidence codes

Structural Evidence

- Use AlphaFold2 for novel structural impact analysis

Population Context

- gnomAD frequencies with ancestry-specific data

Actionable Output

- Clear recommendations, not just classifications

English-first queries

- Always use English terms in tool calls; respond in user's language

Workflow Overview

Phase 1: VARIANT IDENTITY → Normalize HGVS, map gene/transcript/consequence

Phase 2: CLINICAL DATABASES → ClinVar, gnomAD, OMIM, ClinGen, COSMIC, SpliceAI

Phase 2.5: REGULATORY CONTEXT → ChIPAtlas, ENCODE (non-coding variants only)

Phase 3: COMPUTATIONAL PREDICTIONS → CADD, AlphaMissense, EVE, SIFT/PolyPhen

Phase 4: STRUCTURAL ANALYSIS → PDB/AlphaFold2, domains, functional sites (VUS/novel)

Phase 4.5: EXPRESSION CONTEXT → CELLxGENE, GTEx tissue expression

Phase 5: LITERATURE EVIDENCE → PubMed, EuropePMC, BioRxiv, MedRxiv

Phase 6: ACMG CLASSIFICATION → Evidence codes, classification, recommendations

Phase 1: Variant Identity

Tools:

myvariant_query

,

Ensembl_get_variant_info

,

NCBI_gene_search

Capture: HGVS notation (c. and p.), gene symbol, canonical transcript (MANE Select), consequence type, amino acid change, exon/intron location.

Phase 2: Clinical Databases

Tools:

clinvar_search

,

gnomad_search

,

OMIM_search

,

OMIM_get_entry

,

ClinGen_search_gene_validity

,

ClinGen_search_dosage_sensitivity

,

ClinGen_search_actionability

,

COSMIC_search_mutations

,

COSMIC_get_mutations_by_gene

,

DisGeNET_search_gene

,

DisGeNET_get_vda

,

SpliceAI_predict_splice

,

SpliceAI_get_max_delta

Use SpliceAI for: intronic variants near splice sites, synonymous variants, exonic variants near splice junctions.

See

CODE_PATTERNS.md

for implementation details.

Phase 2.5: Regulatory Context (Non-Coding Only)

Apply for intronic (non-splice), promoter, UTR, or intergenic variants near disease genes.

Tools:

ChIPAtlas_enrichment_analysis

,

ChIPAtlas_get_peak_data

,

ENCODE_search_experiments

,

ENCODE_get_experiment

Phase 3: Computational Predictions

Tools:

CADD_get_variant_score

(PHRED 0-99),

AlphaMissense_get_variant_score

(0-1, needs UniProt ID),

EVE_get_variant_score

(0-1),

myvariant_query

(SIFT/PolyPhen),

Ensembl_get_variant_info

(VEP)

Consensus: Run CADD (all variants) + AlphaMissense + EVE (missense). 2+ concordant damaging = strong PP3; 2+ concordant benign = strong BP4.

See

ACMG_CLASSIFICATION.md

for thresholds.

Phase 4: Structural Analysis (VUS/Novel Missense)

Tools:

PDB_search_by_uniprot

,

NvidiaNIM_alphafold2

,

alphafold_get_prediction

,

InterPro_get_protein_domains

,

UniProt_get_protein_function

Workflow: Get structure -> map residue -> assess domain/functional site -> predict destabilization.

Phase 4.5: Expression Context

Tools:

CELLxGENE_get_expression_data

,

CELLxGENE_get_cell_metadata

,

GTEx_get_median_gene_expression

Confirms gene expression in disease-relevant tissues. Supports PP4 if highly restricted; challenges classification if not expressed in affected tissue.

Phase 5: Literature Evidence

Tools:

PubMed_search

,

EuropePMC_search

,

BioRxiv_search_preprints

,

MedRxiv_search_preprints

,

openalex_search_works

,

SemanticScholar_search_papers

Always flag preprints as NOT peer-reviewed.

Phase 6: ACMG Classification

Apply all relevant evidence codes (PVS1, PS1, PS3, PM1, PM2, PM5, PP3, PP5 for pathogenic; BA1, BS1, BS3, BP4, BP7 for benign). See

ACMG_CLASSIFICATION.md

for the complete algorithm.

Special Scenarios

Novel Missense VUS

Check PM5 (other pathogenic at same residue), get AlphaFold2 structure, apply PM1/PP3 as appropriate.

Truncating Variant

Check LOF mechanism, NMD escape, alternative isoforms, ClinGen LOF curation. Apply PVS1 at appropriate strength.

Splice Variant

Run SpliceAI, assess canonical splice distance, in-frame skipping potential. Apply PP3/BP7 based on scores. Output Structure

Variant Interpretation Report: {GENE} {VARIANT}

Executive Summary

1. Variant Identity

1. Population Data

1. Clinical Database Evidence

1. Computational Predictions

1. Structural Analysis

1. Literature Evidence

1. ACMG Classification

1. Clinical Recommendations

1. Limitations & Uncertainties

Data Sources

File naming:

{GENE}_{VARIANT}_interpretation_report.md

Clinical Recommendations

Pathogenic/Likely Pathogenic

Enhanced screening, risk-reducing options, drug dosing adjustment, reproductive counseling, family cascade screening.

VUS

Do not use for medical decisions. Reinterpret in 1-2 years. Pursue functional studies and segregation data.

Benign/Likely Benign

Not expected to cause disease. No cascade testing needed. Quantified Minimums Section Requirement Population frequency gnomAD overall + at least 3 ancestry groups Predictions At least 3 computational predictors Literature search At least 2 search strategies ACMG codes All applicable codes listed References ACMG_CLASSIFICATION.md - Evidence codes, classification algorithm, prediction thresholds, structural/regulatory impact tables CODE_PATTERNS.md - Reusable code patterns for each workflow phase CHECKLIST.md - Pre-delivery verification EXAMPLES.md - Sample interpretations TOOLS_REFERENCE.md - Tool parameters and fallbacks