rs774726264

chr2-151602602-G-A

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6_Very_Strong BP7

The NM_001164507.2(NEB):c.13353C>T(p.Ala4451=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

• Frequency:
  • Genomes: 𝑓 0.091 (1 hom., cov: 0)
  • Exomes 𝑓: 0.44 (197 hom.)
  • Failed GnomAD Quality Control
• Consequence: NEB NM_001164507.2 synonymous
• Clinical Significance: Benign/Likely benign criteria provided, multiple submitters, no conflicts B:7
• Conservation: PhyloP100: -1.79

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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BP6: Variant 2-151602602-G-A is Benign according to our data. Variant chr2-151602602-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 227727.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-151602602-G-A is described in Lovd as [Likely_benign]. Variant chr2-151602602-G-A is described in Lovd as [Benign].
• BP7: Synonymous conserved (PhyloP=-1.79 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NEB	NM_001164507.2	c.13353C>T	p.Ala4451=	synonymous_variant	87/182	ENST00000427231.7
NEB	NM_001164508.2	c.13353C>T	p.Ala4451=	synonymous_variant	87/182	ENST00000397345.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NEB	ENST00000397345.8	c.13353C>T	p.Ala4451=	synonymous_variant	87/182	5	NM_001164508.2	P5
NEB	ENST00000427231.7	c.13353C>T	p.Ala4451=	synonymous_variant	87/182	5	NM_001164507.2	A2
NEB	ENST00000409198.5	c.11601+7207C>T		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.00 AC: 2 AN: 22 Hom.: 1 Cov.: 0 FAILED QC

Gnomad AFR 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: 1.00

Gnomad NFE AF: 0.00

GnomAD3 exomes AF: 0.333 AC: 2 AN: 6 Hom.: 1 AF XY: 0.333 AC XY: 2 AN XY: 6

Gnomad AFR exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 1.00

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.445 AC: 418 AN: 940 Hom.: 197 Cov.: 0 AF XY: 0.435 AC XY: 220 AN XY: 506

Gnomad4 AFR exome AF: 0.250

Gnomad4 AMR exome AF: 0.0400

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0568

Gnomad4 FIN exome AF: 0.982

Gnomad4 NFE exome AF: 0.0968

Gnomad4 OTH exome AF: 0.100

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0909 AC: 2 AN: 22 Hom.: 1 Cov.: 0 AF XY: 0.167 AC XY: 2 AN XY: 12

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: 1.00

Gnomad4 NFE AF: 0.00

Alfa AF: 0.483 Hom.: 644

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:4

Likely benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Likely benign, no assertion criteria provided	clinical testing	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	-	- -
Likely benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -
Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Apr 02, 2021	- -

not specified Benign:2

Likely benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Dec 19, 2014	NEB exons 82-105 are organized in three repetitive blocks of 8 exons each and be cause these blocks are nearly identical in sequence, homologous exons (e.g., exo ns 82, 90, and 98) are co-amplified and sequenced (each amplicon consists of 6 a lleles). This variant represents a nonhomologous position within the three repet itive blocks (c.13353C, c.14811T, and c.16269T). The variable alleles at this po sition are not expected to have clinical significance because these alleles do n ot alter an amino acid residue and are not located within the splice consensus s equence. -
Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -

Nemaline myopathy 2 Benign:1

Likely benign, no assertion criteria provided

clinical testing

Natera, Inc.

Sep 16, 2020

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	3.3
Dann	Benign	0.35

Splicing

Name	Calibrated prediction	Score	Prediction
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: rs774726264; hg19: chr2-152459116; COSMIC: COSV99417924;