rs786204576

Positions:

• chr2-151674475-AC-CA

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1_Moderate PM2 PP5_Very_Strong

The NM_001164508.2(NEB):​c.3987+1_3987+2delinsTG variant causes a splice donor change. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency: Genomes: not found (cov: 31)
• Consequence: NEB NM_001164508.2 splice_donor
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:5
• Conservation: PhyloP100: 6.53

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]

ACMG classification

Verdict is Pathogenic. Variant got 12 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.0041832826 fraction of the gene. Cryptic splice site detected, with MaxEntScore 3.3, offset of 17, new splice context is: tagGTgaag. Cryptic site results in frameshift change. If cryptic site found is not functional and variant results in exon loss, it results in inframe change.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 2-151674475-AC-CA is Pathogenic according to our data. Variant chr2-151674475-AC-CA is described in ClinVar as [Likely_pathogenic]. Clinvar id is 188944.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NEB	NM_001164507.2	c.3987+1_3987+2delinsTG		splice_donor_variant		ENST00000427231.7	NP_001157979.2
NEB	NM_001164508.2	c.3987+1_3987+2delinsTG		splice_donor_variant		ENST00000397345.8	NP_001157980.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NEB	ENST00000397345.8	c.3987+1_3987+2delinsTG		splice_donor_variant		5	NM_001164508.2	ENSP00000380505	P5
NEB	ENST00000427231.7	c.3987+1_3987+2delinsTG		splice_donor_variant		5	NM_001164507.2	ENSP00000416578	A2
NEB	ENST00000409198.5	c.3987+1_3987+2delinsTG		splice_donor_variant		5		ENSP00000386259

Frequencies

GnomAD3 genomes Cov.: 31

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 31

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:5

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Nemaline myopathy 2 Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jul 18, 2023	For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 188944). Disruption of this splice site has been observed in individuals with nemaline myopathy (PMID: 25205138). Information on the frequency of this variant in the gnomAD database is not available, as this variant may be reported differently in the database. This sequence change affects a splice site in intron 36 of the NEB gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in NEB are known to be pathogenic (PMID: 25205138). -
Likely pathogenic, criteria provided, single submitter	literature only	Counsyl	Aug 27, 2014	- -

Nemaline myopathy Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

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

Jul 25, 2022

Variant summary: NEB c.3987+1_3987+2delinsTG is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: 4/4 predict the variant abolishes a 5' splicing donor site. However, these predictions have yet to be confirmed by functional studies. The variant allele, which consists of two single nucleotide changes in cis (c.3987+1G>T and c.3987+2T>G), was found at a frequency of 1.8e-05 in 280626 control chromosomes (gnomAD v2.1). The variant c.3987+1_3987+2delinsTG (also described as c.3987+1_3987+2inv) has been reported in the literature in multiple families / individuals affected with Nemaline Myopathy 2 (Lehtokari_2006, Lehtokari_2014, Ravenscroft_2020). These data indicate that the variant is likely to be associated with the disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Another variant affecting the same splice site was also reported in multiple affected individuals (Lehtokari_2014). Three ClinVar submitters (evaluation after 2014) cite the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

not provided Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Sep 01, 2015

The c. 3987+1_3987+2delGTinsTG splice site variant in the NEB gene destroys the canonical splice donor site of intron 36. It is predicted to cause abnormal gene splicing, either leading to an abnormal message that is subject to nonsense-mediated mRNA decay, or to an abnormal protein product if the message is used for protein translation. The c.3987+1_3987_2delGTinsTG was previously reported, using alternative nomenclature, in a family with nemaline myopathy, although a second pathogenic variant in NEB was not identified (Lehtokari et al., 2006). The c.3987+1_3987+2delGTinsTG variant was not observed in approximately 6,000 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. Additionally, other pathogenic splice site variants in the NEB gene have been reported in the Human Gene Mutation Database in association with nemaline myopathy (Stenson et al., 2014). Therefore, we interpret c.3987+1_3987+2delGTinsTG as a pathogenic variant. -

Arthrogryposis multiplex congenita 6 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

Mar 16, 2024

- -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs786204576; hg19: chr2-152530989;