Table 3

Proposed classification of PALB2 splice site variants according to the ACMG-AMP-2015 guidelines (based solely on location and MAF)

Splice site variantPredicted RNA products/coding potential*PVS1*gnomAD†PM2†Classification‡
LoF* Uncertain*
E1 donorc.48+1,2∆(E1q17)§WarrantedYesLikely pathogenic
E2 acceptorc.49–1,2∆(E2p6)§Not warrantedNFE (1allele)Yes Uncertain significance
E2 donorc.108+1,2∆(E2)/▼(I2)WarrantedYesLikely pathogenic
E3 acceptorc.109–1,2▼(E3p36)/∆(E3)WarrantedYesLikely pathogenic
E3 donorc.211+1,2∆(E3)WarrantedYesLikely pathogenic
E4 acceptorc.212–1,2∆(E4_E5)†WarrantedNFE (1 allele)YesLikely pathogenic
E4 donorc.1684+1,2∆(E4_E5)†WarrantedYesLikely pathogenic
E5 acceptorc.1685–1,2∆(E5)∆(E5p24)Not warrantedNFE (1 allele)Yes Uncertain significance
E5 donorc.2514+1,2∆(E5)WarrantedSAS (1 allele)YesLikely pathogenic
E6 acceptorc.2515–1,2∆(E6)†WarrantedAMR (1 allele)YesLikely pathogenic
E6 donorc.2586+1,2∆(E6)†WarrantedSAS (1 allele)YesLikely pathogenic
E7 acceptorc.2587–1,2▼(E7p20)/∆(E7p2)/∆(E7p10)/∆(E7p25)/∆(E7)▼(E7p42)Not warrantedSAS (1allele)Yes Uncertain significance
E7 donorc.2748+1,2∆(E7)§WarrantedNFE (1 allele)YesLikely pathogenic
E8 acceptorc.2749–1,2▼(E8p30)/∆(E8)WarrantedYesLikely pathogenic
E8 donorc.2834+1,2∆(E8)WarrantedYesLikely pathogenic
E9 acceptorc.2835–1,2∆(E9p30)§/∆(E9)§WarrantedYesLikely pathogenic
E9 donorc.2996+1,2∆(E9)/∆(E9_E10)WarrantedYesLikely pathogenic
E10 acceptorc.2997–1,2∆(E10p2)/∆(E9_E10)/∆(E10)∆(E10p3)Not warrantedSAS (1 allele)Yes Uncertain significance
E10 donorc.3113+1,2∆(E10q31)§/∆(E9_E10)§/∆(E10)§WarrantedYesLikely pathogenic
E11 acceptorc.3114–1,2∆(E11)/∆(E11p2)/∆(E11p23)/∆(E11_E12)WarrantedYesLikely pathogenic
E11 donorc.3201+1,2∆(E11)/∆(E11_E12)WarrantedYesLikely pathogenic
E12 acceptorc.3202–1,2▼(E12p65)/∆(E12p136)/∆(E11_E12)/∆(E12)WarrantedYesLikely pathogenic
E12 donorc.3350+1,2∆(E11_E12)§/∆(E12)§-WarrantedYesLikely pathogenic
E13 acceptorc.3351–1,2WarrantedYesLikely pathogenic
  • *If available (§), predictions on possible RNA products are based on splicing assays performed in representative examples of splice site variants (see online supplementary table 4). If not, predictions are based on the possible upregulation of naturally occurring alternate gene transcripts. Predicted RNA products are classified according to their coding potential as loss-of-function (LoF) or uncertain (the possibility of coding for a functional or partially functional protein cannot be disregarded). If only LoF transcripts are predicted, we assume that PVS1 is warranted. If ≥1 transcript with uncertain coding potential is predicted, we propose that PVS1 (based solely on variant location) is not warranted.

  • †After reviewing gnomAD, we conclude that PM2 is met for all possible splice site variants.

  • ‡According to the ACMG-AMP-2015 guidelines, if PVS1 and PM2 are warranted, splice site variants should be classified as likely pathogenic. Otherwise, splice site variants should be classified as uncertain significance. This analysis has highlighted seven splice site variants in ClinVar needing additional justification for assertion as pathogenic/likely pathogenic (see online supplementary table 5 for further details).

  • ACMG-AMP, American College of Medical Genetics and Genomics-Association for Molecular Pathology; AMR, American; NFE, non-finish Europeans; SAS, South Asia.