Proposed classification of PALB2 splice site variants according to the ACMG-AMP-2015 guidelines (based solely on location and MAF)
| Splice site variant | Predicted RNA products/coding potential* | PVS1* | gnomAD† | PM2† | Classification‡ | ||
| LoF* | Uncertain* | ||||||
| E1 donor | c.48+1,2 | ∆(E1q17)§ | – | Warranted | – | Yes | Likely pathogenic |
| E2 acceptor | c.49–1,2 | – | ∆(E2p6)§ | Not warranted | NFE (1allele) | Yes | Uncertain significance |
| E2 donor | c.108+1,2 | ∆(E2)/▼(I2) | – | Warranted | – | Yes | Likely pathogenic |
| E3 acceptor | c.109–1,2 | ▼(E3p36)/∆(E3) | – | Warranted | – | Yes | Likely pathogenic |
| E3 donor | c.211+1,2 | ∆(E3) | – | Warranted | – | Yes | Likely pathogenic |
| E4 acceptor | c.212–1,2 | ∆(E4_E5)† | – | Warranted | NFE (1 allele) | Yes | Likely pathogenic |
| E4 donor | c.1684+1,2 | ∆(E4_E5)† | – | Warranted | – | Yes | Likely pathogenic |
| E5 acceptor | c.1685–1,2 | ∆(E5) | ∆(E5p24) | Not warranted | NFE (1 allele) | Yes | Uncertain significance |
| E5 donor | c.2514+1,2 | ∆(E5) | – | Warranted | SAS (1 allele) | Yes | Likely pathogenic |
| E6 acceptor | c.2515–1,2 | ∆(E6)† | – | Warranted | AMR (1 allele) | Yes | Likely pathogenic |
| E6 donor | c.2586+1,2 | ∆(E6)† | – | Warranted | SAS (1 allele) | Yes | Likely pathogenic |
| E7 acceptor | c.2587–1,2 | ▼(E7p20)/∆(E7p2)/∆(E7p10)/∆(E7p25)/∆(E7) | ▼(E7p42) | Not warranted | SAS (1allele) | Yes | Uncertain significance |
| E7 donor | c.2748+1,2 | ∆(E7)§ | – | Warranted | NFE (1 allele) | Yes | Likely pathogenic |
| E8 acceptor | c.2749–1,2 | ▼(E8p30)/∆(E8) | – | Warranted | – | Yes | Likely pathogenic |
| E8 donor | c.2834+1,2 | ∆(E8) | – | Warranted | – | Yes | Likely pathogenic |
| E9 acceptor | c.2835–1,2 | ∆(E9p30)§/∆(E9)§ | – | Warranted | – | Yes | Likely pathogenic |
| E9 donor | c.2996+1,2 | ∆(E9)/∆(E9_E10) | – | Warranted | – | Yes | Likely pathogenic |
| E10 acceptor | c.2997–1,2 | ∆(E10p2)/∆(E9_E10)/∆(E10) | ∆(E10p3) | Not warranted | SAS (1 allele) | Yes | Uncertain significance |
| E10 donor | c.3113+1,2 | ∆(E10q31)§/∆(E9_E10)§/∆(E10)§ | – | Warranted | – | Yes | Likely pathogenic |
| E11 acceptor | c.3114–1,2 | ∆(E11)/∆(E11p2)/∆(E11p23)/∆(E11_E12) | – | Warranted | – | Yes | Likely pathogenic |
| E11 donor | c.3201+1,2 | ∆(E11)/∆(E11_E12) | – | Warranted | – | Yes | Likely pathogenic |
| E12 acceptor | c.3202–1,2 | ▼(E12p65)/∆(E12p136)/∆(E11_E12)/∆(E12) | – | Warranted | – | Yes | Likely pathogenic |
| E12 donor | c.3350+1,2 | ∆(E11_E12)§/∆(E12)§- | Warranted | – | Yes | Likely pathogenic | |
| E13 acceptor | c.3351–1,2 | – | – | Warranted | – | Yes | Likely 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.