BRCA1_FINAL_MERGED_EVIDENCE_10082026.xlsx

	A	B	C	D	E	F	G	H	I	J	K	L	M	N	O	P	Q	R	S	T
1	Evidence category	Evidence Points (EP)
2	Consensus allocatable evidence points for pathogenicity (missense validation)	4.1
3	Consensus allocatable evidence points for benignity (missense validation)	-4.2
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5	Truthset combinations yielding maximal score (Censored)
6	Set name	Pathogenic source set	Benign source set	EP-PS3	EP-BS3	# Classified (truthsets)		Assay result						FP rate (FP / (FP+TN))	FN rate (FN / (FN+TP))	P1 prior	P2 posterior path	P2 posterior benign	OddsPath (deleterious)	OddsPath (neutral)
7						Pathogenic	Benign	Deleterious		Intermediate		Neutral
8						Pathogenic	Benign	Path (TP)	Benign (FP)	Path	Benign	Path (FN)	Benign (TN)
9	Optimal missense truthset	gnomAD v4.1 benign (BA1, BS1, BS1_sup) OR in-silico benign + ClinVar missense; >=2 stars; P/LP and B/LB	gnomAD v4.1 benign (BA1, BS1, BS1_sup) OR in-silico benign + ClinVar missense; >=2 stars; P/LP and B/LB	4.1	-4.2	45	65	44	2	0	1	1	62	3.1%	2.2%	0.409	0.936	0.031	21.185	0.047
10	Optimal all variants truthset	ClinVar all variants; >=2 stars; P/LP and B/LB	ClinVar all variants; any stars; P/LP, B/LB and conflicting	4.5	-5.6	120	146	117	4	2	5	1	137	2.8%	0.8%	0.451	0.959	0.014	28.47	0.018
11	Optimal all variants truthset	ClinVar all variants; >=2 stars; P/LP and B/LB	ClinVar all variants; any stars; P/LP and B/LB	4.5	-5.6	120	146	117	4	2	5	1	137	2.8%	0.8%	0.451	0.959	0.014	28.47	0.018
12	Optimal PTV + synonymous truthset	Systematically-generated: Synonymous + SpliceAI + truncating pathogenic + NMD threshold	Systematically-generated: Synonymous + SpliceAI + truncating pathogenic + NMD threshold	7	-6.5	116	508	116	2	0	8	0	498	0.4%	0.0%	0.186	0.975	0.002	169.333	0.009
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