NEB p.Ser6648=

The NM_001164508.2(NEB):c.19944G>A (p.Ser6648=) variant in NEB is a synonymous variant located at the intron exon boundary of exon 129. mRNA characterization of homozygous probands displayed that the variant abolishes the normal donor splice site, shifting towards the use of an alternative (cryptic) splice site in intron 129 which causes a partial intronic retention of 120bp that creates a premature stop codon and shorter polypeptide (PS3) (PMID: 26841830, PMID: 25205138). The computational splicing predictor SpliceAI gives a score of 0.77 for donor loss, predicting splice site disruption (PP3). The highest population minor allele frequency in gnomAD v4.1.0 is 0.0001659 (1/6026) alleles) in an unspecified ethnic group (no population codes met). This variant has been identified in at least 9 probands in either a homozygous state or with a second likely pathogenic, pathogenic, or rare uncertain variant (PM3_Strong) (PMID 26841830, 36233295, 25205138, 36233295, 37460656, 32222963, 36714460). At least one proband homozygous for the variant had an affected sibling also homozygous for the variant (PP1) (PMID: 37460656). Nemaline rods have been observed in at least one proband identified with the variant (PP4) (PMID: 26841830). In summary, this variant meets the criteria to be classified as pathogenic for Nemaline Myopathy for autosomal recessive inheritance based on the ACMG/AMP criteria applied as specified by the ClinGen Congenital Myopathy VCEP: (PS3, PM3_Strong, PP4, PP3, PP1); ClinGen Congenital Myopathies VCEP Specifications version 1.0.0; 5/12/2025)