Table 1.

Pathogenicity criteria for two variants not reported in the ClinVar database according to ACMG standards and guidelines [11]

Evidence of pathogenicity	Fulfilled criteria with explanation	g.5884G > T	g.11895_11898del
Moderate evidence	PM2 – the prevalence of the variants in affected individuals is significantly increased compared with the prevalence in controls	1) The variant was not found in 180 healthy Latvian control chromosomes 2) 0.00004119 (for Europeans in ExAC database)	1) The variant was not found in 180 healthy Latvian control chromosomes 2) Not reporteda
	PM3 – for recessive disorders, detected in trans with a pathogenic allele	Located in trans position with other allele (in our case likely pathogenic allele)	Located in trans position with other allele (in our case likely pathogenic allele)
Supporting evidence	PP3 – multiple lines of computational evidence support a deleterious effect on the gene product	1) HSF – predicted WT donor site broken ΔCT- -13.62%b (max entropy − 67.38%c) 2) Mutalyzer – variant located near to splice site 3) MutationTaster – disease causing (protein features (might be) affected; splice site change)	1) HSF – predicted WT donor site broken ΔCT-55.3%b (max entropy − 284.9%c) 2) Mutalyzer - variant located in splice site 3) MutationTaster – disease causing (protein features (might be) affected; splice site change)
	PP4 – patient’s phenotype or family history is highly specific for disease with single genetic etiology	Yes	Yes
	PP5 – reputable source recently reports variant as pathogenic, but the evidence is not available to the laboratory to perform an independent evaluation	Passuello et al., 2009	None
Total score		Likely pathogenic	Likely pathogenic

^aAs identified variant is indel frequency, should be evaluated with caution

^b ΔCT – if difference between consensus value for wild type and mutated variantis below − 10% it is considered that splice site is broken [7]

^cif maximal entropy is below − 30%, it is considered that splice site is broken [7]