Nonsense and frameshift variants
Only one patient was carrier of the recurrent CHEK2 c.1100delC mutation, p.(Thr367Metfs*15) (1 out of 2,346, 0.04%). Given the great amount of data related to CHEK2 c.1100delC, this variant meets PS3 (well established functional studies) and PS4 (higher prevalence in affected individuals versus controls), besides PVS1. However, PS4 was assigned with moderate strength (PS4_moderate), since OR>5.0 for a moderately penetrant gene cannot be achieved. The combination of these rules classified this variant as pathogenic (P) in any combination of rules framework, and since it is well-studied and frequent in some populations, it was classified as established risk allele (ERA) within the Senol-Cosar framework (Table 1 and Table S2). c.1368dupA, p.(Glu457Argfs*33) variant meets PS3 and PM2_supporting, being classified as P in all frameworks. c.715G>T, p.(Glu239*) variant meets PM2, therefore was classified as likely pathogenic (LP) using ACMG and ClinGen-TP53 frameworks. According to Tavtigian’s Bayes model (Tavtigian et al., 2018), it gathers enough evidence to be classified as P. Variants c.279G>A, p.(Trp93*) and c.591delA, p.(Val198Phefs*7) were weighted PM2_supporting. The sum of PVS1 and a supporting criterion is not enough to classify a variant as LP/P using ACMG guidelines (S. Richards et al., 2015). However, application of Bayesian modelling of this combination of rules gives a posterior probability of 0.988, resulting in its classification as LP according to Tavtigian’s (S. Richards et al., 2015; Tavtigian et al., 2018) as well as following ClinGen-TP53 modifications (ClinGen-TP53_Expert_Panel, 2019).