rs113095802

chr2-151724252-A-G

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BS1 BS2

The NM_001164507.2(NEB):c.612+8T>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0188 in 1,605,928 control chromosomes in the GnomAD database, including 372 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.024 (60 hom., cov: 31)
  • Exomes 𝑓: 0.018 (312 hom.)
• Consequence: NEB NM_001164507.2 splice_region, intron
• Scores: Splicing: ADA: 0.00002785
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:11
• Conservation: PhyloP100: 0.343

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 Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 2-151724252-A-G is Benign according to our data. Variant chr2-151724252-A-G is described in ClinVar as [Benign]. Clinvar id is 129753.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-151724252-A-G is described in Lovd as [Benign]. Variant chr2-151724252-A-G is described in Lovd as [Likely_benign].
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0235 (3584/152198) while in subpopulation AFR AF= 0.0397 (1650/41538). AF 95% confidence interval is 0.0381. There are 60 homozygotes in gnomad4. There are 1712 alleles in male gnomad4 subpopulation. Median coverage is 31. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 60 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NEB	NM_001164507.2	c.612+8T>C		splice_region_variant, intron_variant		ENST00000427231.7
NEB	NM_001164508.2	c.612+8T>C		splice_region_variant, intron_variant		ENST00000397345.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NEB	ENST00000397345.8	c.612+8T>C		splice_region_variant, intron_variant		5	NM_001164508.2	P5
NEB	ENST00000427231.7	c.612+8T>C		splice_region_variant, intron_variant		5	NM_001164507.2	A2
NEB	ENST00000409198.5	c.612+8T>C		splice_region_variant, intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.0235 AC: 3570 AN: 152080 Hom.: 60 Cov.: 31

Gnomad AFR AF: 0.0396

Gnomad AMI AF: 0.0242

Gnomad AMR AF: 0.0151

Gnomad ASJ AF: 0.0430

Gnomad EAS AF: 0.00462

Gnomad SAS AF: 0.0239

Gnomad FIN AF: 0.0120

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0176

Gnomad OTH AF: 0.0269

GnomAD3 exomes AF: 0.0186 AC: 4556 AN: 244552 Hom.: 56 AF XY: 0.0194 AC XY: 2567 AN XY: 132312

Gnomad AFR exome AF: 0.0407

Gnomad AMR exome AF: 0.00822

Gnomad ASJ exome AF: 0.0468

Gnomad EAS exome AF: 0.00417

Gnomad SAS exome AF: 0.0290

Gnomad FIN exome AF: 0.0127

Gnomad NFE exome AF: 0.0170

Gnomad OTH exome AF: 0.0187

GnomAD4 exome AF: 0.0183 AC: 26561 AN: 1453730 Hom.: 312 Cov.: 29 AF XY: 0.0187 AC XY: 13496 AN XY: 723124

Gnomad4 AFR exome AF: 0.0429

Gnomad4 AMR exome AF: 0.00880

Gnomad4 ASJ exome AF: 0.0472

Gnomad4 EAS exome AF: 0.00184

Gnomad4 SAS exome AF: 0.0301

Gnomad4 FIN exome AF: 0.0123

Gnomad4 NFE exome AF: 0.0168

Gnomad4 OTH exome AF: 0.0238

GnomAD4 genome AF: 0.0235 AC: 3584 AN: 152198 Hom.: 60 Cov.: 31 AF XY: 0.0230 AC XY: 1712 AN XY: 74410

Gnomad4 AFR AF: 0.0397

Gnomad4 AMR AF: 0.0150

Gnomad4 ASJ AF: 0.0430

Gnomad4 EAS AF: 0.00463

Gnomad4 SAS AF: 0.0247

Gnomad4 FIN AF: 0.0120

Gnomad4 NFE AF: 0.0176

Gnomad4 OTH AF: 0.0266

Alfa AF: 0.0224 Hom.: 17

Bravo AF: 0.0236

Asia WGS AF: 0.0320 AC: 112 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:11

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Benign:7

Likely benign, no assertion criteria provided	clinical testing	Genetic Services Laboratory, University of Chicago	-	Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed. -
Benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Jan 13, 2015	c.612+8T>C in intron 8 of NEB: This variant is not expected to have clinical sig nificance because it is not located within the conserved splice consensus sequen ce. It has been identified in 3.7% (148/3974) of African American chromosomes fr om a broad population by the NHLBI Exome Sequencing Project (http://evs.gs.washi ngton.edu/EVS; dbSNP rs113095802). -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 12, 2016	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Apr 01, 2019	Variant summary: NEB c.612+8T>C alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.019 in 272532 control chromosomes in the gnomAD database, including 70 homozygotes. The observed variant frequency is approximately 5 fold of the estimated maximal expected allele frequency for a pathogenic variant in NEB causing Nemaline Myopathy 2 phenotype (0.0035), strongly suggesting that the variant is benign. To our knowledge, no occurrence of c.612+8T>C in individuals affected with Nemaline Myopathy 2 and no experimental evidence demonstrating its impact on protein function have been reported. Five clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as benign/likely benign. Based on the evidence outlined above, the variant was classified as benign. -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -
Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Sep 28, 2020	- -

Nemaline myopathy 2 Benign:3

Benign, criteria provided, single submitter	clinical testing	Invitae	Feb 01, 2024	- -
Benign, no assertion criteria provided	clinical testing	Natera, Inc.	Sep 16, 2020	- -
Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 13, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

not provided Benign:1

Likely benign, no assertion criteria provided

clinical testing

Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	1.5
Dann	Benign	0.55

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000028
dbscSNV1_RF	Benign	0.066
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs113095802; hg19: chr2-152580766;