Table 2. Comparison of SpliceAI-predicted and experimentally demonstrated functional effects of the 19 engineered GT>GC (+2T>C) substitutions that generated wild-type transcripts.

Gene Symbol	mRNA Reference	Chromosome	hg38 Coordinate	Reference Sequence	Substitutiona	Generation of Wild-type Transcriptsb	SpliceAI Delta Score of Donor Loss
							+2T>C	+2T>A	+2T>G
CCDC103	NM_213607.2	17	44899861	T	IVS1+2T>C	Yes	0.82	0.82	0.82
DBI	NM_001079862.2	2	119368307	T	IVS2+2T>C	Yes	0.86	1	1
DNAJC19	NM_145261.3	3	180985924	A	IVS5+2T>C	Yes (42%)	0.03	0.99	0.95
FATE1	NM_033085.2	X	151716227	T	IVS1+2T>C	Yes (84%)	0.08	0.96	1
FOLR3	NM_000804.3	11	72139484	T	IVS4+2T>C	Yes	0.45	1	1
HESX1	NM_003865.2	3	57199760	A	IVS1+2T>C	Yes (2%)	0.81	0.98	0.98
IFNL2	NM_172138.1	19	39269823	T	IVS5+2T>C	Yes (5%)	0.05	0.84	0.73
IL10	NM_000572.3	1	206770905	A	IVS3+2T>C	Yes	0.61	1	1
MGP	NM_000900.4	12	14884211	A	IVS2+2T>C	Yes (80%)	0.97	0.99	0.99
PSMC5	NM_001199163.1	17	63830503	T	IVS6+2T>C	Yes (56%)	0.31	0.98	1
			63831228	T	IVS8+2T>C	Yes (56%)	0.21	1	1
			63831618	T	IVS10+2T>C	Yes (46%)	0.83	1	1
RPL11	NM_000975.5	1	23692761	T	IVS2+2T>C	Yes	0	0.87	0.86
			23693915	T	IVS3+2T>C	Yes	0.74	1	1
RPS27	NM_001030.4	1	153991225	T	IVS2+2T>C	Yes (63%)	0.67	1	1
			153991678	T	IVS3+2T>C	Yes	0.98	1	1
SELENOS	NM_203472.2	15	101277340	A	IVS1+2T>C	Yes	0.81	1	1
			101274418	A	IVS5+2T>C	Yes (14%)	0.79	1	1
SPINK1	NM_003122.3	5	147828020	A	IVS3+2T>Cc	Yes	0.35	0.99	1

^aIn accordance with the traditional IVS (InterVening Sequence; i.e., an intron) nomenclature as previously described [16].

^bExpression level (in parentheses), determined by quantitative RT-PCR analysis, was available for all +2T>C substitutions that generated only wild-type transcripts under the experimental conditions described in [16].

^cIdentical to the SPINK1 c.194+2T>C variant in Supplementary Table S1 ^{(1.2MB, pdf)} and Table 1.