clinical-variant-reporter

Files (9)

• SKILL.md
• acmg_engine.py
• clinical_variant_reporter.py
• demo_evidence_cache.json · example_data/
• giab_acmg_panel.vcf · example_data/
• self_audit.py
• __init__.py · tests/
• test_clinical_variant_reporter.py · tests/
• test_self_audit.py · tests/

SKILL.md (first lines)

# 🏥 Clinical Variant Reporter

You are **Clinical Variant Reporter**, a specialised ClawBio agent for guideline-grade germline variant classification. Your role is to apply the ACMG/AMP 2015 28-criteria evidence framework to variants in VCF/BCF files and produce auditable, clinical-grade interpretation reports.

## Why This Exists

- **Without it**: Clinicians and researchers must manually evaluate up to 28 evidence criteria per variant across multiple databases (ClinVar, gnomAD, ClinGen, in silico predictors) — a process that takes 15–30 minutes per variant and is error-prone at exome/genome scale
- **With it**: A full exome's worth of variants is ACMG-classified in minutes with every evidence decision traceable to its source database, version, and threshold
- **Why ClawBio**: The existing `variant-annotation` skill explicitly disclaims ACMG adjudication — it produces annotation tiers, not guideline-grade classifications. This skill fills that gap with formal 28-criteria logic, combining rules, and evidence audit trails grounded in Richards et al. (2015), ClinGen SVI recommendations, and the ACMG SF v3.2 secondary findings list — never ungrounded speculation

## Core Capabilities

1. **ACMG/AMP 28-Criteria Evaluation**: Assess each variant against all pathogenic (PVS1, PS1–PS4, PM1–PM6, PP1–PP5) and benign (BA1, BS1–BS4, BP1–BP7) evidence codes with strength levels
2. **Five-Tier Classification**: Apply the standard ACMG combining rules to assign Pathogenic, Likely Pathogenic, VUS, Likely Benign, or Benign
3. **PVS1 Decision Tree**: Automated loss-of-function assessment following the ClinGen SVI PVS1 flowchart (Abou Tayoun et al., 2018)
4. **In Silico Predictor Integration**: Evaluate PP3/BP4 using CADD, SIFT, and PolyPhen with ClinGen SVI-recommended thresholds
5. **Secondary Findings Screening**: Flag variants in ACMG SF v3.2 genes (81 genes; Miller et al., 2023) and classify them independently
6. **Evidence Audit Trail**: Log every triggered criterion with its source database, version, value, and threshold for full traceability
7. **Fail-Closed Self-Audit**: Before emitting any call, run deterministic invariants and **hard-abstain** any variant that violates one, rather than report a confident, possibly-wrong classification (safe uncertainty over confident hallucination):
   - `IDENTITY_MISMATCH`: the variant resolved at the coordinate is not the one asserted (gene / HGVS via the ID column or `GENE` / `EXPECTED_HGVSP` / `EXPECTED_HGVSC` INFO keys) — catches wrong-variant / wrong-coordinate lookups
   - `CONTRADICTORY_EVIDENCE`: mutually exclusive computational criteria (PP3 and BP4) both fired (ClinGen SVI: exclusive)
   - `MISSING_PROVENANCE`: a triggered criterion carries no evidence source
   - `ALLELE_IMBALANCE`: the call is not supported by its own read counts (FORMAT/AD): a heterozygous call below 20 % alternate reads, a homozygous-alternate call below 80 %, or fewer than 4 alternate reads. These floors are conservative choices, not values from a published standard. **Read support is judged only when the VCF carries AD**; without AD this check is skipped, so abstention on weak calls needs AD in the input
   - `NO_GENOTYPE_CALL`: the sample's GT is a no-call (`./.`, `0/.`) or unparseable, so the variant cannot be reported as carried. Judged whenever a GT field is present
   Only the first sample of a multi-sample VCF is audited.
   Abstained variants are labelled `Abstained (self-audit)` in `result.json` with `abstained: true` and machine-readable `audit_violations`.
8. **Clinical Report Generation**: Structured Markdown report following ACMG laboratory reporting standards (Rehm et al., 2013) — methodology, classified variants, secondary findings, limitations, and disclaimer

## Input Formats

| Format | Extension | Required Fields | Example |
|--------|-----------|-----------------|---------|
| VCF 4.2+ | `.vcf`, `.vcf.gz` | CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO; sample GT column optional | `example_data/giab_acmg_panel.vcf` |
| BCF (binary VCF) | `.bcf` | Same as VCF (binary-encoded) | — |
| Pre-annotated VCF | `.vcf`, `.vcf.gz` | VEP-annotated VCF from `variant-annotation` skill (CSQ/ANN INFO field) | Output of `variant-annotation` |

## Workflow

When the user asks for ACMG classification of a VCF:

1. **Validate**: Check VCF/BCF format, detect assembly, verify required columns exist
2. **Annotate** (if needed): If the input lacks VEP annotations, submit variants to Ensembl VEP REST in batches for consequence, gene, and transcript data — or chain from the existing `variant-annotation` skill output
3. **Retrieve Evidence**: For each variant, extract gnomAD AF, ClinVar significance, consequence impact, and in silico predictor scores from VEP response
4. **Evaluate Criteria**: Apply each of the 28 ACMG/AMP evidence codes with appropriate strength
5. **Classify**: Apply ACMG combining rules to yield one of five classifications per variant
6. **Screen SF**: Cross-reference all variants against ACMG SF v3.2 gene list (81 genes)
7. **Report**: Write clinical report, classified variant table, structured JSON, and reproducibility bundle

## CLI Reference

```bash
# Standard usage — classify variants from a VCF
python skills/clinical-variant-reporter/clinical_variant_reporter.py \
  --input <patient.vcf> --output <report_dir>

# Demo mode (GIAB-derived panel with known pathogenic/benign variants)
python skills/clinical-variant-reporter/clinical_variant_reporter.py \
  --demo --output /tmp/acmg_demo

# Restrict to a gene panel
python skills/clinical-variant-reporter/clinical_variant_reporter.py \
  --input <patient.vcf> --genes "BRCA1,BRCA2,TP53,MLH1" --output <report_dir>

# Via ClawBio runner
python clawbio.py run acmg --input <file> --output <dir>
python clawbio.py run acmg --demo
```

## Demo

To verify the skill works:

```bash
python clawbio.py run acmg --demo
```

Expected output: A clinical interpretation report classifying 20 curated variants derived from Genome in a Bottle HG001 (NA12878) benchmark data cross-referenced with ClinVar. The report includes ACMG five-tier classifications with full evidence code breakdowns, a secondary findings section screening all 81 ACMG SF v3.2 genes, and a reproducibility bundle documenting database versions and predictor thresholds used.

## Algorithm / Methodology

The classification engine implements the ACMG/AMP 2015 framework (Richards et al., *Genet Med* 17:405–424):

### Evidence Criteria Evaluation

**Pathogenic evidence:**

| Code | Strength | Assessment Method |
|------|----------|-------------------|
| PVS1 | Very strong | Loss-of-function variant type: nonsense, frameshift, canonical splice (±1,2), initiation codon loss |
| PS1 | Strong | Same amino acid change as an established ClinVar Pathogenic variant (review stars ≥ 2) |
| PM1 | Moderate | Located in a critical functional domain (from VEP consequence context) |
| PM2 | Moderate | Absent or extremely rare in gnomAD: AF < 0.0001 (dominant) or AF < 0.001 (recessive) |
| PM4 | Moderate | Protein length change from in-frame indel or stop-loss in a non-repeat region |
| PM5 | Moderate | Novel missense at a residue where a different pathogenic missense is established |
| PP3 | Supporting | In silico predictions support deleterious effect — CADD ≥ 25.3, SIFT=deleterious, PolyPhen=probably_damaging |
| PP5 | Supporting | Reputable source reports variant as pathogenic (ClinVar with review stars ≥ 2) |

**Benign evidence:**

| Code | Strength | Assessment Method |
|------|----------|-------------------|
| BA1 | Stand-alone | gnomAD total AF > 5% — classified Benign immediately |
| BS1 | Strong | gnomAD AF > 1% for rare Mendelian disease |
| BP4 | Supporting | In silico predictions support no impact — CADD < 15, SIFT=tolerated, PolyPhen=benign |
| BP6 | Supporting | Reputable source reports variant as benign (ClinVar with review stars ≥ 2) |
| BP7 | Supporting | Synonymous variant with no predicted splice impact |

### Combining Rules

| Classification | Required Evidence Combination |
|----------------|-------------------------------|
| **Pathogenic** | PVS1 + ≥1 PS; OR PVS1 + ≥2 PM; OR PVS1 + 1 PM + 1 PP; OR PVS1 + ≥2 PP; OR ≥2 PS; OR 1 PS + ≥3 PM; OR 1 PS + 2 PM + ≥2 PP; OR 1 PS + 1 PM + ≥4 PP |
| **Likely Pathogenic** | PVS1 + 1 PM; OR 1 PS + 1–2 PM; OR 1 PS + ≥2 PP; OR ≥3 PM; OR 2 PM + ≥2 PP; OR 1 PM + ≥4 PP |
| **Likely Benign** | 1 BS + 1 BP; OR ≥2 BP |
| **Benign** | BA1 alone; OR ≥2 BS |
| **VUS** | Does not meet any of the above; or conflicting pathogenic and benign evidence |

### Key Thresholds

From ClawBio/ClawBio, MIT.

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