Submissions for variant NM_001164508.2(NEB):c.19944G>A (p.Ser6648=)

gnomAD frequency: 0.00001  dbSNP: rs201553266

Total submissions: 14

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	RCV000224886	SCV000280967	pathogenic	not provided	2014-08-13	criteria provided, single submitter	clinical testing
GeneDx	RCV000224886	SCV000329870	pathogenic	not provided	2025-02-24	criteria provided, single submitter	clinical testing	RNA studies demonstrate a disruption of the canonical splice site resulting in a premature termination codon and thus a shortened nebulin protein (PMID: 26841830); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports a deleterious effect on splicing; This variant is associated with the following publications: (PMID: 25205138, 26841830, 32721234, 17576681, 9536098, 39194158, 37460656, 36233295, 35081925, 39802796, 36714460, 38280421, 32222963, 26403434)
Labcorp Genetics (formerly Invitae), Labcorp	RCV000541914	SCV000640653	pathogenic	Nemaline myopathy 2	2024-12-09	criteria provided, single submitter	clinical testing	This sequence change affects codon 6648 of the NEB mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the NEB protein. This variant also falls at the last nucleotide of exon 129, which is part of the consensus splice site for this exon. This variant is present in population databases (rs201553266, gnomAD 0.01%). This variant has been observed in individuals with nemaline myopathy (PMID: 25205148; internal data). ClinVar contains an entry for this variant (Variation ID: 235402). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
Ambry Genetics	RCV000622763	SCV000740914	likely pathogenic	Inborn genetic diseases	2015-06-12	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000780536	SCV000917874	pathogenic	Nemaline myopathy	2018-06-12	criteria provided, single submitter	clinical testing	Variant summary: NEB c.19944G>A (p.Ser6648Ser) alters a non-conserved nucleotide that is the last nucleotide of an exon and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: Three predict the variant abolishes a 5' splicing donor site, while two predict the variant weakens a 5' donor site. These predictions are supported by functional evidence reported by Oliveira_2016 using whole blood from a homozygous patient, which showed the preferential use of a cryptic splice site, leading to a predicted truncation of the protein. Truncations downstream of this variant have been classified as pathogenic by our laboratory (e.g., p.Arg7026X and p.Leu8137fsX18). The variant allele was found at a frequency of 2.9e-05 in 245250 control chromosomes, which does not exceed the maximal expected allele frequency for a pathogenic variant in NEB. c.19944G>A has been reported in the literature in several individuals affected with Nemaline Myopathy 2, including both homozygous and compound heterozygous patients, indicating that the variant is likely to be associated with disease. Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 with conflicting assessments, including pathogenic (1x), likely pathogenic (2x), and VUS (1x). Based on the evidence outlined above, the variant was classified as pathogenic.
DASA	RCV001836641	SCV002097273	pathogenic	Arthrogryposis multiplex congenita 6	2022-02-14	criteria provided, single submitter	clinical testing	This sequence change has been observed in affected individual(s) and ClinVar contains an entry for this variant (ClinVar ID: 235402; PMID: 9536098; 17576681; 32721234; 32222963; 26841830; 26403434; 25205138) - PS4. The variant is present at low allele frequencies population databases (rs201553266 - gnomAD 0.00006573%; ABraOM no frequency - http://abraom.ib.usp.br/) - PM2_supporting. The p.(Ser6648=) was detected in trans with a pathogenic variant (PMID: 9536098; 17576681; 32721234) - PM3_strong. Multiple lines of computational evidence support a deleterious effect on the gene or gene product - PP3. In summary, the currently available evidence indicates that the variant is pathogenic.
PreventionGenetics, part of Exact Sciences	RCV004547569	SCV004117601	pathogenic	NEB-related disorder	2023-05-26	criteria provided, single submitter	clinical testing	The NEB c.19944G>A variant is not predicted to result in an amino acid change (p.=). This variant is predicted to abolish the adjacent splice donor site (Alamut Visual Plus v1.6.1). This variant has been reported along with a second putative disease-causing variant in multiple individuals with nemaline myopathy; in most cases parental testing confirmed the variants were on opposite alleles (Lehtokari et al 2014. PubMed ID: 25205138; Wang Q et al 2020. PubMed ID: 32222963; Zhang Y et al 2022. PubMed ID: 35081925). This variant is reported in 0.011% of alleles in individuals of East Asian descent in gnomAD (http://gnomad.broadinstitute.org/variant/2-152408252-C-T). This variant is interpreted as pathogenic.
Baylor Genetics	RCV001836641	SCV004200141	pathogenic	Arthrogryposis multiplex congenita 6	2024-03-09	criteria provided, single submitter	clinical testing
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	RCV000541914	SCV005399062	pathogenic	Nemaline myopathy 2	2024-10-09	criteria provided, single submitter	clinical testing	Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with arthrogryposis multiplex congenita 6 (MIM#619334) and nemaline myopathy 2 (MIM#256030). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0210 - Splice site variant proven to affect splicing of the transcript with known effect on protein sequence. RT-PCR studies on blood from an individual homozygous for this variant have shown it causes loss of the canonical donor splice site, and gain of a cryptic splice site in the intron. This causes the retention of 120 intronic nucleotides creating a premature stop codon that is expected to lead to nonsense-mediated decay (PMID: 26841830). (SP) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD (v2) <0.01 for a recessive condition (7 heterozygotes, 0 homozygotes). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been classified as pathogenic or likely pathogenic by multiple clinical laboratories in ClinVar, and has been observed as homozygous or compound heterozygous in individuals with congenital myopathy in the literature (PMIDs: 26841830, 35081925). (SP) 1205 - This variant has been shown to be maternally inherited (by trio analysis). (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign
Juno Genomics, Hangzhou Juno Genomics, Inc	RCV004796118	SCV005417135	pathogenic	Nemaline myopathy 2; Arthrogryposis multiplex congenita 6		criteria provided, single submitter	clinical testing	PS3+PM2_Supporting+PM3_Strong+PP4
Fulgent Genetics, Fulgent Genetics	RCV004796118	SCV005650419	pathogenic	Nemaline myopathy 2; Arthrogryposis multiplex congenita 6	2024-06-06	criteria provided, single submitter	clinical testing
Eurofins Ntd Llc (ga)	RCV000224886	SCV000705513	uncertain significance	not provided	2017-02-24	flagged submission	clinical testing
Counsyl	RCV000541914	SCV001132257	likely pathogenic	Nemaline myopathy 2	2018-07-30	no assertion criteria provided	clinical testing
Muscle and Diseases Team, Institut de Génétique et Biologie Moléculaire et Cellulaire	RCV000541914	SCV005038602	uncertain significance	Nemaline myopathy 2	2024-03-01	flagged submission	research	PM3+PM2+PP3