rs201553266

Variant names:

Variant summary

Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM2PP3_StrongPP5_Very_Strong

The NM_004543.5(NEB):c.14841G>A(p.Ser4947Ser) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,612,444 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★).

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)

Exomes 𝑓: 0.000014 ( 0 hom. )

Consequence

NEB
NM_004543.5 splice_region, synonymous

Scores

Splicing: ADA: 0.9999

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:13U:2

Conservation

PhyloP100: 0.745

Variant links:

Genes affected

NEB (HGNC:7720): (nebulin) This gene encodes nebulin, a giant protein component of the cytoskeletal matrix that coexists with the thick and thin filaments within the sarcomeres of skeletal muscle. In most vertebrates, nebulin accounts for 3 to 4% of the total myofibrillar protein. The encoded protein contains approximately 30-amino acid long modules that can be classified into 7 types and other repeated modules. Protein isoform sizes vary from 600 to 800 kD due to alternative splicing that is tissue-, species-,and developmental stage-specific. Of the 183 exons in the nebulin gene, at least 43 are alternatively spliced, although exons 143 and 144 are not found in the same transcript. Of the several thousand transcript variants predicted for nebulin, the RefSeq Project has decided to create three representative RefSeq records. Mutations in this gene are associated with recessive nemaline myopathy. [provided by RefSeq, Sep 2009]

NEB links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 14 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

PP3

Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF, max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.

PP5

Variant 2-151551738-C-T is Pathogenic according to our data. Variant chr2-151551738-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 235402.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-151551738-C-T is described in Lovd as [Pathogenic]. Variant chr2-151551738-C-T is described in Lovd as [Likely_pathogenic]. Variant chr2-151551738-C-T is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NEB	NM_001164507.2 link	c.19944G>A	p.Ser6648Ser	synonymous_variant	Exon 129 of 182	ENST00000427231.7	NP_001157979.2
NEB	NM_001164508.2 link	c.19944G>A	p.Ser6648Ser	synonymous_variant	Exon 129 of 182	ENST00000397345.8	NP_001157980.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NEB	ENST00000397345.8 link	c.19944G>A	p.Ser6648Ser	synonymous_variant	Exon 129 of 182	5	NM_001164508.2	ENSP00000380505.3		P20929-2
NEB	ENST00000427231.7 link	c.19944G>A	p.Ser6648Ser	synonymous_variant	Exon 129 of 182	5	NM_001164507.2	ENSP00000416578.2		P20929-3

Frequencies

GnomAD3 genomes

AF:

0.00000657

AC:

AN:

152136

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000147

Gnomad OTH

AF:

0.00

GnomAD3 exomes

AF:

0.0000282

AC:

AN:

248206

Hom.:

AF XY:

0.0000297

AC XY:

AN XY:

134644

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.0000582

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.000112

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000178

Gnomad OTH exome

AF:

0.000166

GnomAD4 exome

AF:

0.0000144

AC:

AN:

1460308

Hom.:

Cov.:

AF XY:

0.0000138

AC XY:

AN XY:

726526

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.0000896

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.0000505

Gnomad4 SAS exome

AF:

0.0000116

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000108

Gnomad4 OTH exome

AF:

0.0000332

GnomAD4 genome

AF:

0.00000657

AC:

AN:

152136

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

74306

show subpopulations

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.0000147

Gnomad4 OTH

AF:

0.00

Bravo

AF:

0.0000189

EpiCase

AF:

0.00

EpiControl

AF:

0.0000593

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:13Uncertain:2

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

Nemaline myopathy 2

Pathogenic:3Uncertain:1

Jul 30, 2018

Counsyl

Significance: Likely pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Mar 01, 2024

Muscle and Diseases Team, Institut de Génétique et Biologie Moléculaire et Cellulaire

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: research

PM3+PM2+PP3 -

Oct 09, 2024

Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: 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 -

Dec 09, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: 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. -

not provided

Pathogenic:2Uncertain:1

Aug 13, 2014

Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 24, 2025

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: 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) -

Feb 24, 2017

Eurofins Ntd Llc (ga)

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Nemaline myopathy

Pathogenic:2

Jun 12, 2018

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: 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. -

Mar 07, 2025

Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: curation

The p.Ser6648= variant in NEB has been reported in at least 10 individuals with nemaline myopathy (PMID: 25205138, 26403434, 26841830, 32222963, 36233295, 37460656, 36714460), and has been identified in 0.007% (4/59922) of Latino/Admixed American chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP ID: rs201553266). Although this variant has been seen in the general population in a heterozygous state, its frequency is low enough to be consistent with a recessive carrier frequency. This variant has also been reported in ClinVar (Variation ID: 235402) and has been interpreted as pathogenic/likely pathogenic by multiple submitters, and as a variant of uncertain significance by Eurofins Ntd Llc (ga). Of the ten affected individuals, seven were compound heterozygotes that carried a reported likely pathogenic variant in trans or with unknown phase and two were homozygotes, which increases the likelihood that the p.Ser6648= variant is pathogenic (Variation ID: 190457; PMID: 25205138, 26403434, 26841830, 32222963, 36233295, 37460656, 36714460). mRNA analysis performed on unaffected tissues shows possible evidence of intron retention after exon 129. This variant is located in the last three bases of the exon, which is part of the 5' splice region. Computational tools do suggest an impact to splicing. However, this information is not predictive enough to determine/rule out pathogenicity. The phenotype of individuals heterozygous for this variant are highly specific for nemaline myopathy based on the presence of nemaline rods consistent with disease. In summary, although additional studies are required to fully establish its clinical significance, this variant is likely pathogenic for autosomal recessive nemaline myopathy. ACMG/AMP Criteria applied: PM3_strong, PVS1_moderate, PP4, PM2_supporting (Richards 2015). -

Arthrogryposis multiplex congenita 6

Pathogenic:2

Feb 14, 2022

DASA

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: 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. -

Mar 09, 2024

Baylor Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Nemaline myopathy 2;C5543431:Arthrogryposis multiplex congenita 6

Pathogenic:2

Juno Genomics, Hangzhou Juno Genomics, Inc

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PS3+PM2_Supporting+PM3_Strong+PP4 -

Jun 06, 2024

Fulgent Genetics, Fulgent Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Inborn genetic diseases

Pathogenic:1

Jun 12, 2015

Ambry Genetics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

NEB-related disorder

Pathogenic:1

May 26, 2023

PreventionGenetics, part of Exact Sciences

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: 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. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.34

CADD

Benign

DANN

Benign

0.53

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Pathogenic

1.0

dbscSNV1_RF

Pathogenic

0.98

SpliceAI score (max)

0.77

Details are displayed if max score is > 0.2

DS_DL_spliceai

0.77

Position offset: 0

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over