drug-discovery-prompts/upstream/mims-harvard-ToolUniverse/skills/tooluniverse-variant-interpretation/CHECKLIST.md

title, task, lineage_type, upstream_source, upstream_sha, imported_at, prompt_class, upstream_changes, author, validated

title	task	lineage_type	upstream_source	upstream_sha	imported_at	prompt_class	upstream_changes	author	validated
Clinical Variant Interpreter Checklist		import	https://github.com/mims-harvard/ToolUniverse/blob/e2520a96/skills/tooluniverse-variant-interpretation/CHECKLIST.md	e2520a96	2026-06-26	prompt	accepted	upstream	false

Clinical Variant Interpreter Checklist

Pre-delivery verification checklist for variant interpretation reports.

Report Quality Checklist

Structure & Format

• Report file created: {GENE}_{VARIANT}_interpretation_report.md
• All 9 main sections present
• Executive summary completed (not [Interpreting...])
• Data sources section populated

Phase 1: Variant Identity

• Gene symbol identified
• HGVS c. notation provided
• HGVS p. notation (if applicable)
• Transcript ID (MANE Select preferred)
• Consequence type identified
• Exon/intron location stated
• Amino acid change (for missense)

Phase 2: Population Data

• gnomAD queried
• Overall allele frequency reported
• ≥3 ancestry-specific frequencies
• Homozygote count reported
• Hemizygote count (X-linked genes)
• Frequency interpreted vs. disease prevalence

Phase 3: Clinical Database Evidence

• ClinVar searched
• Classification reported (or "Not in ClinVar")
• Review status noted (gold stars)
• Number of submissions documented
• Conflicting interpretations noted (if any)
• OMIM gene-disease associations checked
• ClinGen gene validity (if available)

Phase 4: Computational Predictions

• ≥3 predictors reported
• SIFT score and interpretation
• PolyPhen-2 score and interpretation
• CADD score (raw and phred)
• Concordance assessed (agree/disagree)
• PP3 or BP4 applied appropriately

Phase 5: Structural Analysis (for missense)

• Protein structure source identified (PDB/AlphaFold)
• pLDDT at variant position (if AlphaFold)
• Residue location (buried/surface)
• Secondary structure context
• Domain/functional site proximity
• PM1 consideration documented

Phase 6: Literature Evidence

• PubMed searched with ≥2 strategies
• Functional studies documented (or "None found")
• Case reports documented
• PS3 consideration documented
• PP1 (segregation) documented if available

Phase 7: ACMG Classification

• All evidence codes explicitly listed
• Each code has strength modifier
• Code justification provided
• Classification calculated correctly
• Classification stated in executive summary

Phase 8: Clinical Recommendations

• Recommendations appropriate to classification
• VUS: No medical decisions
• Pathogenic: Specific follow-up
• Family screening addressed

Phase 9: Limitations

• Missing data acknowledged
• Conflicting evidence noted
• Uncertainty quantified

---

Citation Requirements

Every Evidence Statement Must Include

• Source database/tool in backticks
• Specific identifier (ClinVar ID, PMID)
• Date of access (for changing databases)

Format Examples

*Source: ClinVar VCV000012345, reviewed 4-star, accessed 2026-02-04*
*Source: gnomAD v4.0, overall AF=0.00001, accessed 2026-02-04*
*Source: PMID 12345678 - functional study showed loss of activity*
*Source: AlphaFold DB via `alphafold_get_prediction`, pLDDT=92 at position*

---

ACMG Code Verification

For Each Code Applied

• Code abbreviation correct (PVS1, PM2, PP3, etc.)
• Strength appropriate (VeryStrong/Strong/Moderate/Supporting)
• Evidence clearly supports application
• Not double-counted

Common Errors to Avoid

• PM2 without checking gnomAD
• PP3 without multiple concordant predictions
• PVS1 for non-null variants
• PS3 without true functional evidence
• Applying same evidence to multiple codes

---

Classification Calculation

Verify Math

Classification	Minimum Evidence
Pathogenic	≥1 VeryStrong + ≥1 Strong/Moderate
Likely Pathogenic	≥1 Strong + ≥2 Moderate
VUS	Insufficient evidence
Likely Benign	≥1 Strong + ≥1 Supporting (benign)
Benign	≥1 StandAlone OR ≥2 Strong (benign)

Classification Cross-Check

• Evidence codes align with final classification
• No conflicting codes ignored
• Classification matches standard algorithms

---

Evidence Grading

All Classifications Must Have

• Classification tier: ★★★, ★★☆, ★☆☆, or VUS
• Evidence strength description
• Key supporting evidence highlighted

Tier Definitions

Tier	Symbol	Criteria
High confidence	★★★	Multiple independent lines, no conflicts
Moderate confidence	★★☆	Good evidence, minor gaps
Limited confidence	★☆☆	Minimal evidence, apply with caution
Uncertain	VUS	Insufficient to classify

---

Quantified Minimums

Section	Minimum Requirement
Population frequencies	gnomAD + ≥3 ancestry groups
Computational predictors	≥3 tools
Literature searches	≥2 search strategies
ACMG codes	All applicable documented
Clinical recommendations	≥1 per classification type

---

Structural Analysis Quality (for Missense)

Must Include

• Structure source (PDB ID or "AlphaFold predicted")
• pLDDT at position (if AlphaFold)
• Residue depth/accessibility
• Structural consequence prediction

Quality Thresholds

Metric	Confident	Uncertain
pLDDT	>70	<70
PDB Resolution	<3.0 Å	>3.0 Å

---

Special Scenario Checks

Truncating Variants

• NMD prediction assessed
• LOF mechanism confirmed for gene
• PVS1 strength correctly applied
• Last exon exception considered

Splice Variants

• Canonical splice site distance
• SpliceAI scores (if available)
• In-frame skip assessment
• PVS1 modified if warranted

X-linked Genes

• Sex of individual considered
• Hemizygote frequency used appropriately
• Penetrance in females addressed

---

Output Files

Required

• {GENE}_{VARIANT}_interpretation_report.md - Main report

Optional Data Export

• {GENE}_{VARIANT}_evidence_table.csv - Structured evidence
• {GENE}_{VARIANT}_acmg_codes.csv - Applied codes

---

Final Review

Before Delivery

• No [Interpreting...] placeholders remaining
• All tables properly formatted
• Executive summary synthesizes findings
• Classification stated prominently
• Clinical recommendations actionable
• Limitations clearly stated

Common Issues to Avoid

• Missing gnomAD frequencies
• Classification without evidence codes
• Recommendations not matching classification
• Missing literature search
• Structure analysis skipped for VUS missense
• ACMG codes without justification

---

ClinVar-Specific Checks

When Variant in ClinVar

• VCV ID documented
• Review status (stars) noted
• Number of submitters
• Date of last evaluation
• Concordance with our assessment

When Variant NOT in ClinVar

• Explicitly state "Not in ClinVar as of {date}"
• Consider novel variant workflow
• Emphasize structural analysis

---

Tool Verification Checklist

Before Report Generation

• ClinVar_search_variants returns results or "not found"
• gnomad_search_variants frequency values valid
• MyVariant_query_variants predictions populated
• Structure available (PDB or AlphaFold)

NVIDIA NIM Availability

• Check if structural analysis needed
• Confirm NVIDIA_API_KEY if using NvidiaNIM_alphafold2
• Document if fallback used

---

Recommendations Matrix

Match Recommendations to Classification

Classification	Testing	Management	Family
Pathogenic	Confirm	Specific action	Cascade
Likely Path	Confirm	Specific action	Cascade
VUS	Monitor	Clinical judgment	Not for testing
Likely Benign	No repeat	Reassurance	Not needed
Benign	No repeat	Reassurance	Not needed

---

Report Completeness Score

Calculate before delivery:

Section	Points
Variant identity complete	10
gnomAD with ancestry	10
ClinVar documented	10
≥3 predictors	10
Structural analysis	15
Literature search	10
ACMG codes with rationale	20
Clinical recommendations	10
Limitations stated	5

Minimum passing score: 85/100