Table 2.

PS1 code weights for variants with same predicted splicing event as a known (likely) pathogenic variant

Variant under assessment (VUA)	Baseline computational/predictive code applicable to VUA	Position of comparison variant relative to VUA	PS1 code applicable to VUA
			with P comparison variant	with LP comparison variant
Located outside splice donor/acceptor ±1,2 dinucleotide positions	PP3	same nucleotide	PS1	PS1_Moderate
	PP3	within same splice donor/acceptor motif (including at ±1,2 positions)	PS1_Moderate	PS1_Supporting
Located at splice donor/acceptor ±1,2 dinucleotide positions	PVS1	within same splice donor/acceptor ±1,2 dinucleotide	PS1_Supporting	N/A
	PVS1	within same splice donor/acceptor region, but outside ±1,2 dinucleotidea	PS1_Supporting	PS1_Supporting
	PVS1_Strong, PVS1_Moderate, or PVS1_Supporting	within same splice donor/acceptor ±1,2 dinucleotide	PS1	N/A
	PVS1_Strong, PVS1_Moderate, or PVS1_Supporting	within same splice donor/acceptor motif, but outside ±1,2 dinucleotidea	PS1_Moderate	PS1_Supporting

Prerequisite for all: the predicted event of the VUA must precisely match the predicted event of the comparison (likely) pathogenic variant (e.g., both predicted to lead to exon skipping, or both to lead to enhanced use of a cryptic splice motif, AND the strength of the prediction for the VUA must be of similar or higher strength than the strength of the prediction for the comparison [likely] pathogenic variant). For an exonic variant, predicted or proven functional effect of missense substitution(s) encoded by the VUA and (likely) pathogenic variant should also be considered before application of this code. Dinucleotide positions refer to donor and acceptor dinucleotides in reference transcript(s) used for curation. Designated donor and acceptor motif ranges should be based on position weight matrices for intron category (see methods). For GT-AG introns these are defined as follows: the donor motif, last 3 bases of the exon and 6 nucleotides of intronic sequence adjacent to the exon; acceptor motif, first base of the exon and 20 nucleotides upstream from the exon boundary. Consider other motif ranges for non-GT-AG introns.

^aIf relevant, splicing assay data for a pathogenic variant outside a ±1,2 dinucleotide position may be used to update a PVS1 decision tree and hence the applicable PVS1 code for a ±1,2 dinucleotide variant.