Table 2 Performance of six tools on three biological tasks

Method	Task 1^a		Task 2: Positional diagnosis^b							Task 3: Diagnosis with noisy background^c
		Adj^d	UC	WC	LC	Pro	5'U	ups	int	UC	WC	LC	Pro	5'U	ups	int
CADD	o	>10 bp	+++	++	+	++	+	++	+++	++	+	−	+	+	o	+
CATO	–	>1 kbp	+	+	+	+	+	+	+	−	−	−	−	−	−	−
DeepSEA	o	>10 bp	+++	+++	+	+++	++	+++	+++	+++	+	o	++	+	+	+
EIGEN	–	>100 bp	++	++	+	++	+	++	++	+	+	o	o	+	+	o
GWAVA	–	>50 bp	−	−	−	−	−	−	−	+	+	+	++	++	+	−
LINSIGHT	–	>10 bp	+++	++	+	+++	+	++	++	+++	+	−	++	+	+	+

Pathogenic variants are defined by location in ultra-conserved (UC), well-conserved (WC), or least-conserved (LC) intervals, or by location in the promoter (pro), 5’UTR (5’U), upstream gene region (ups) or intron (int)
^a– indicates pathogenic scores are not specific to alleles at the same position, o indicates allele-specific scores but with low discriminative power
^bsuccess rates are indicated by: − (<50%), o (50–60%), + (60–80%), ++ (80–90%), +++ (>90%)
^cnon-pathogenic vs. pathogenic ratios are indicated by: − (<1:1), o (1–2:1), + (2–10:1), ++ (10–20:1), +++ (>20:1)
^dAdj refers to adjacency corresponding to the minimum distance between pairs of pathogenic and non-pathogenic variants for which significantly different scores are produced in Task 2

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