Table 1.

Predicted spliceogenic candidate causal GWAS SNPs and their predicted functional consequences

SNP	Effect allele frequency	HGVS (MANE select transcript)	SpliceAI max delta score	Predicted mRNA splicing effecta	Predicted functional consequenceb	Ensembl- annotated alternative exon
rs7177179	0.25	ENST00000263791.10(EIF2AK4):c.2767–1183T>C	0.17	107 bp alternative exon	p.(Lys923fs)	no
rs7173595	0.69	ENST00000396402.6(CYP19A1):c.145+1229G>A	0.01	100 bp alternative exon	p.(Gly49fs)	no
rs28518777	0.34	ENST00000396402.6(CYP19A1):c.–38–18360C>T	0.02	199 bp alternative exon	5′ UTR insertion	no
rs35888506	0.45	ENST00000358273.9(NF1):c.4836–1609C>T	0.11	97 bp alternative exon	p.(Phe1613fs)	yes
rs2854320	0.50	ENST00000358273.9(NF1):c.8377+6342C>A	0.01	54 bp alternative exon	p.(Pro2792_Gly2793ins18)	yes
rs7502834	0.45	ENST00000358273.9(NF1):c.8377+1709G>A	0.02	77 bp alternative exon	p.(Gly2793fs)	yes
rs2278868	0.56	ENST00000336915.11(SKAP1):c.481G>A	0.07	125 bp exon skipping	p.(Ser148fs)	yes

HGVS, Human Genome Variation Society; MANE, Matched Annotation from NCBI and EMBL-EBI.

^aPredicted by the SpliceAI-10k calculator.

^bPredicted consequence for the canonical protein isoforms were derived from the results of the SpliceAI-10k calculator.