PolyClip-T — Variant Analysis

🧬 Variant Prototype Shared — applied to all modes

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Prototype presets

Filter rules — all rules applied additively

Minimum evidence score to report variant

Threshold: 3 points

Category	Points	Logic / flag
Germline pathogenicity	+2 ACMG pass +1–2 Tiered	GERM_PASS = 1 → +2 pts GERM_TIER = 1 → +2 pts \| GERM_TIER = 2 → +1 pt
Somatic second-hit	+3 Strict +1 Supporting	TWO_HIT_STRICT = 1 → +3 pts Supporting evidence (no strict flag) → +1 pt
Family segregation	+1–3 Co-segregation +1–2 Family-level	Quantitative co-segregation score (configured below)
Biological context	+1 × 2	PATHWAY_HIT = 1 → +1 pt DNA repair pathway (optional) → +1 pt
Multi-compartment origin	+1	ORIGIN_PROFILE = both → +1 pt (Germline–somatic co-occurrence)
Fallback evidence	+1	Variant shared among ≥ 2 affected relatives — linked by AND / OR rules below

📝Paste Tab-Separated Variants

Required columns (tab-separated, header row optional):
CHROM · POS · REF · ALT · Gene_name

Variant rows

0 rows

📄Upload .txt / .tsv File

File format: Tab-separated with optional header row.
Columns: CHROM · POS · REF · ALT · Gene_name

📂

Drop file here or click to browse

.txt · .tsv — tab-separated

Case 3 mode: Configure patients below, then expand ⚖️ Evidence Scoring Rules above to customise point thresholds and fallback AND/OR logic. Output is a structured JSON with per-patient variant lists and applied scoring metadata.

👨‍👩‍👧Patient Configuration