Table 1.

Splicing-relevant modifications to the PVS1 decision tree of Abou Tayoun et al (2018)²

Original Abou Tayoun et al PVS1 decision tree	New recommendations	Example in Figure 1
Splicing alterations at 5′ (or 3′) UTRs are not specifically addressed	Annotate as PVS1_N/A unless the splicing outcome is predicted to impact protein or elements proven critical for function and/or expression.	A
Apply PVS1_Moderate if there are no alternative start codons in the transcript set for a gene, for a start loss variant if one or more Pathogenic variant(s) have been reported 5′ of the next downstream putative in-frame start codon.	Consider upweighting based on the frame of alternative start sites, their location relative to known clinically important functional domains, and/or location of Pathogenic variants 3′ to the native start site and 5′ to the next putative in-frame alternative start site.	B
Apply PVS1_Strong for single- to multi-exon deletions that preserve reading frame, and truncated/altered region is critical to protein function. Relevant domain indicated by experimental evidence proving a critical role of the domain and/or presence of non-truncating pathogenic variants in the region.	Consider upweighting to PVS1 if the in-frame deletion removes a protein region critical to function e.g. Pathogenic missense variant has been identified in that protein domain.	F
If >10% of the protein is removed, apply PVS1_Strong, regardless of whether the region is critical to protein function.	Consider upweighting to PVS1 if the truncated protein region is critical to function e.g. Pathogenic missense variant has been identified in that protein domain or complementary splice site Pathogenic variation.	H