Table 3.

A comparison of ClassifyCNV and AnnotSV.

		ClassifyCNV (%)	AnnotSV (%)
Pathogenic/likely pathogenic	Sensitivity	60.9	100
	Specificity	98.4	19.7
	Accuracy	88.1	41.7
	% Benign/likely benign calls	0	0
	% Uncertain calls	39.1	0
Benign/likely benign	Sensitivity	25	37.5
	Specificity	100	92.1
	Accuracy	92.9	86.9
	% Pathogenic/likely pathogenic calls	0	62.5
	% Uncertain calls	75	0
Uncertain significance	Sensitivity	98.1	5.6
	Specificity	51.6	100
	Accuracy	81	40.5

Both tools were tested on a set of 84 variants manually evaluated by ACMG/ClinGen. While ClassifyCNV produced a higher percentage of uncertain calls compared to AnnotSV, it had higher specificity and accuracy for pathogenic/likely pathogenic and benign/likely benign variants.