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. 2024 Oct 28;35(4):102374. doi: 10.1016/j.omtn.2024.102374

Table 2.

Predictions for candidate variants potentially altering splicing

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.