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Table 3 ACMG SF v2.0 genes classified per ACMG/AMP guidelines using InterVar software

From: Prevalence of pathogenic/likely pathogenic variants in the 24 cancer genes of the ACMG Secondary Findings v2.0 list in a large cancer cohort and ethnicity-matched controls

Classification Controls (982 exomes) All cases (1173 exomes) 1 case/family (738 exomes)
  Cancer genes Non-cancer genes Cancer genes Non-cancer genes Cancer genes Non-cancer genes
Pathogenic 4 (17) 0 4 (13) 0 4 (7) 0
Likely pathogenic 0 (0) 8 (8) 0 (0) 11 (17) 0 (0) 10 (11)
Variant of unknown significance 141 (174) 403 (503) 179 (260) 440 (713) 140 (167) 336 (454)
Likely benign 248 (463) 398 (671) 242 (570) 417 (865) 202 (355) 332 (541)
Benign 12 (42) 30 (208) 12 (106) 28 (266) 11 (69) 26 (167)
No classification* 252 (3477) 832 (8181) 290 (4315) 814 (10393) 225 (2714) 668 (6535)
  1. Numbers represent unique variant count and number in parenthesis represents allele counts
  2. *Majority of the “no classification” variants were intronic, 5′/3′ untranslated regions, and 22 indels