Table 2.
Patient | Gene | Variant identified | regSNP - intron |
NNSplice |
MaxEnt |
SpliceAI |
SPiP interp. | SPiP % (rank) | VarSEAK |
Minigene effect | |||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Predict. | WT | MUT | WT | MUT | Var (%) | Score | Class | ||||||
RP-2034 | USH2A | c.5168-26A>C | B | – | – | – | – | – | 0.55 (AL) | BPA | 43.04 (35.2–51.14) | 1 | ES |
RP-1496 | ADGRV1 | c.3443G>A | – | – | – | – | – | – | 0.53 (AG) | NEP | 03.72 (01.51–07.52) | 1 | NE |
RP1950 | USH2A | c.4106C>T | - | - | - | - | - | - | 0.31 (AL) | REA | 54.00 (45.68–62.16) | 1 | ES+NAS |
c.11549-5dup | – | – | – | 8.57 | 2.16 | −74.8 (AL) | – | NEP | 01.85 (00.38–05.32) | 1 | NE | ||
RP-1222 | USH1C | c.1234G>A | – | – | – | – | – | – | 0.31 (AL)/0.34 (DL) | REA | 85.91 (79.27–91.06) | 1 | NE |
RP-1036 | USH2A | c.8681+3960A>G | PD | - | 0.99 (AG) | 1.09 | 9.84 | 802.75 (AG) | 0.98 (AG) | NEP | 00 (00–00.92) | 5 | PEC |
RP-1600 | USH2A | c.15298-1252T>G | B | – | – | −1.63 | 6.97 | 527.61 (AG) | – | NEP | 00 (00–00.92) | 1 | NE |
RP-1943 | USH2A | c.6049+3895G>A | B | – | 0.92 (AG) | 2.44 | 4.93 | 102.05 (AG) | – | NEP | 00 (00–00.92) | 1 | NE |
RP-1455 | USH2A | c.5299-2503A>G | B | – | 0.58 (AG) | −3.79 | 4.96 | 230.87 (AG) | – | NEP | 00.25 (00.01–01.39) | 1 | NE |
RP-1994 | USH2A | c.11389+2566A>G | PD | – | 0.73 (AG) | −0.93 | 7.82 | 940.86 (AG) | – | NEP | 00 (00–00.92) | 1 | NE |
c.11048-2124A>G | PD | – | 0.81 (AG) | −2.14 | 6.61 | 408.88 (AG) | – | NEP | 00 (00–00.92) | 4 | NE | ||
RP-2264 | USH2A | c.7120+4268A>G | D | – | 0.65 (DG) | −4.04 | 4.14 | 202.48 (DG) | – | NEP | 00 (00–00.92) | 1 | NE |
RP-2239 | USH2A | c.7300+8957A>C | B | 0.46 | 0.74(AG) | 6.22 | 5.44 | 19.61 (AG) | – | NEP | 00 (00–00.92) | 1 | NE |
RP-2268 | USH2A | c.6806-810A>G | D | – | 0.92 (DG) | −0.37 | 7.81 | 2210.81 (DG) | – | NEP | 00.5 (00.06–01.78) | 3 | NE |
RP-1815 | USH2A | c.9958+3438A>G | PD | - | 0.98 (AG) | 1.66 | 10.41 | 527.11 (AG) | 0.97 (AG) | NEP | 00 (00–00.92) | 3 | PEC |
c.4628-27169C>G | D | – | 0.57 (DG) | −1.77 | 6.49 | 466.67 (DG) | – | NEP | 00 (00–00.92) | 2 | NE |
For regSNP-intron, NNSplice, and SpliceAI predictors, the scores are given within 0 (benign) to 1 (pathogenic). For VarSEAK the score ranks from 1 (benign) to 5 (pathogenic). Variants highlighted in bold showed an aberrant effect in splicing in the minigene assays. RP, patient number; NT, nucleotide; predict., prediction; B, benign; PD, probably damaging; TPR, true positive ratio; FPR, false positive ratio; WT, wild type; MUT, mutant; AG, acceptor gain; DG, donor gain; Var, variation; AL, acceptor loss; DL, donor loss; Interp., interpretation; BPA, branchpoint alteration; NEP, no effect predicted; REA, regulatory element alteration; ES, exon skipping; NE, no effect; NAS, new acceptor site; PEC, pseudoexon creation.