In order to assist the clinical interpretation of SV, AnnotSV provides on top of the annotations a ranking score to assess SV pathogenicity. This score is an adaptation of the work provided by the joint consensus recommendation of ACMG and ClinGen (Riggs et al., 2020). We especially took attention in scoring as much as possible recessive SV observed in various dataset (NGS, array based...)


0.99 or more points Pathogenic Class 5
0.90 to 0.98 points Likely pathogenic Class 4
0.89 to −0.89 points Variant of uncertain significance Class 3
−0.90 to −0.98 points Likely benign Class 2
−0.99 or fewer points Benign Class 1


The comprehensive and detailed scoring guidelines are available in the Scoring_Criteria_AnnotSV_latest.xlsx file (see Table1 for loss SV and Table2 for gain SV).