Table 1.

In Silico Splice Predictions

Variant (gene; transcript; position)	Acceptor Site Gain	SSF [0-100]	MaxEnt [0-16]	NNSPLICE [0-1]	GeneSplicer [0-15]	SpliceAI [0-1]	Donor Site Gain (SpliceAI)
NR2E3; NM_014249.3; c.1100+1124G>A; g.17:71815241G>A	Position: c.1100+1126	78.36	7.47	0.88	1.67	0.63	Position: c.1100+1214
GPR179; NM_001004334.3; c.903+343G>A; g.15:36494957C>T	Position: c.903+345	90.61	12.24	0.97	9.91	0.86	Position: c.903+542
CNGB3; Transcript NM_019098.4; c.852+4751A>T; g.8:87674402T>A	Position: c.852+4756	83.92	8.08	-	5.97	0.60	Position: c.852+4829

In silico splice prediction scores using Alamut Visual Software included SSF, MaxEnt, NNSPLICE, and GeneSplicer flagged these deep intronic mutations as pathogenic acceptor gain mutations when greater than the default threshold values (SSF ≥70, MaxEnt ≥0, NNSPLICE ≥0.4, GeneSplicer ≥0, SpliceAI ≥0.5). SpliceAI (Illumina) also flagged these mutations as a pathogenic acceptor gain score. These scores also provided predicted aberrant exonization start and end positions. Genomic coordinates refer to the build GRCh37/hg19 for GPR179 and CNGB3, and GRCh38/hg38 for NR2E3.