X-31478314-T-A

Variant names:

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_004006.3(DMD):c.8729A>T(p.Glu2910Val) variant causes a missense change. The variant allele was found at a frequency of 0.0146 in 1,209,357 control chromosomes in the GnomAD database, including 183 homozygotes. There are 5,332 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.028 ( 73 hom., 849 hem., cov: 22)

Exomes 𝑓: 0.013 ( 110 hom. 4483 hem. )

Consequence

DMD
NM_004006.3 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts U:1B:17

Conservation

PhyloP100: 5.93

Variant links:

Genes affected

DMD (HGNC:2928): (dystrophin) This gene spans a genomic range of greater than 2 Mb and encodes a large protein containing an N-terminal actin-binding domain and multiple spectrin repeats. The encoded protein forms a component of the dystrophin-glycoprotein complex (DGC), which bridges the inner cytoskeleton and the extracellular matrix. Deletions, duplications, and point mutations at this gene locus may cause Duchenne muscular dystrophy (DMD), Becker muscular dystrophy (BMD), or cardiomyopathy. Alternative promoter usage and alternative splicing result in numerous distinct transcript variants and protein isoforms for this gene. [provided by RefSeq, Dec 2016]

DMD links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.010023415).

BP6

Variant X-31478314-T-A is Benign according to our data. Variant chrX-31478314-T-A is described in ClinVar as [Likely_benign]. Clinvar id is 11267.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-31478314-T-A is described in Lovd as [Benign]. Variant chrX-31478314-T-A is described in Lovd as [Likely_benign]. Variant chrX-31478314-T-A is described in Lovd as [Pathogenic].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DMD	NM_004006.3 link	c.8729A>T	p.Glu2910Val	missense_variant	Exon 59 of 79	ENST00000357033.9	NP_003997.2	P11532

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DMD	ENST00000357033.9 link	c.8729A>T	p.Glu2910Val	missense_variant	Exon 59 of 79	1	NM_004006.3	ENSP00000354923.3		A0A075B6G3

Frequencies

GnomAD3 genomes

AF:

0.0276

AC:

3070

AN:

111177

Hom.:

Cov.:

AF XY:

0.0253

AC XY:

844

AN XY:

33363

show subpopulations

Gnomad AFR

AF:

0.0669

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0168

Gnomad ASJ

AF:

0.0186

Gnomad EAS

AF:

0.0424

Gnomad SAS

AF:

0.00883

Gnomad FIN

AF:

0.0145

Gnomad MID

AF:

0.0210

Gnomad NFE

AF:

0.00952

Gnomad OTH

AF:

0.0228

GnomAD3 exomes

AF:

0.0209

AC:

3833

AN:

183174

Hom.:

AF XY:

0.0176

AC XY:

1192

AN XY:

67668

show subpopulations

Gnomad AFR exome

AF:

0.0731

Gnomad AMR exome

AF:

0.0243

Gnomad ASJ exome

AF:

0.0168

Gnomad EAS exome

AF:

0.0457

Gnomad SAS exome

AF:

0.0125

Gnomad FIN exome

AF:

0.0194

Gnomad NFE exome

AF:

0.0101

Gnomad OTH exome

AF:

0.0155

GnomAD4 exome

AF:

0.0132

AC:

14526

AN:

1098124

Hom.:

110

Cov.:

AF XY:

0.0123

AC XY:

4483

AN XY:

363480

show subpopulations

Gnomad4 AFR exome

AF:

0.0690

Gnomad4 AMR exome

AF:

0.0243

Gnomad4 ASJ exome

AF:

0.0177

Gnomad4 EAS exome

AF:

0.0417

Gnomad4 SAS exome

AF:

0.0118

Gnomad4 FIN exome

AF:

0.0186

Gnomad4 NFE exome

AF:

0.00951

Gnomad4 OTH exome

AF:

0.0174

GnomAD4 genome

AF:

0.0276

AC:

3075

AN:

111233

Hom.:

Cov.:

AF XY:

0.0254

AC XY:

849

AN XY:

33429

show subpopulations

Gnomad4 AFR

AF:

0.0670

Gnomad4 AMR

AF:

0.0170

Gnomad4 ASJ

AF:

0.0186

Gnomad4 EAS

AF:

0.0422

Gnomad4 SAS

AF:

0.00886

Gnomad4 FIN

AF:

0.0145

Gnomad4 NFE

AF:

0.00953

Gnomad4 OTH

AF:

0.0218

Alfa

AF:

0.0155

Hom.:

365

Bravo

AF:

0.0316

TwinsUK

AF:

0.00998

AC:

ALSPAC

AF:

0.00831

AC:

ESP6500AA

AF:

0.0686

AC:

263

ESP6500EA

AF:

0.00847

AC:

ExAC

AF:

0.0208

AC:

2524

EpiCase

AF:

0.00841

EpiControl

AF:

0.00741

ClinVar

Significance: Benign/Likely benign

Submissions summary: Uncertain:1Benign:17

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:8

Aug 08, 2014

Eurofins Ntd Llc (ga)

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 17, 2014

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Mar 07, 2019

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

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: DMD c.8729A>T (p.Glu2910Val) results in a non-conservative amino acid change located in a spectrin/alpha-actinin repeat (IPR018159) of the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.021 in 199997 control chromosomes in the gnomAD database, including 53 homozygotes and 1379 hemizygotes. The observed variant frequency is significantly higher than expected for a pathogenic variant in DMD causing Dystrophinopathies phenotype, strongly suggesting that the variant is benign. Seven ClinVar submissions from clinical diagnostic laboratories (evaluation after 2014) cite the variant as benign (6x) and once as likely benign. Based on the evidence outlined above, the variant was classified as benign. -

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

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Genome Diagnostics Laboratory, University Medical Center Utrecht

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Mar 21, 2015

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

p.Glu2910Val in exon 59 of DMD: This variant is not expected to have clinical si gnificance because it has been identified in 7.3% (768/10496) of African chromos omes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org/; dbSNP rs41305353). -

Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Duchenne muscular dystrophy

Uncertain:1Benign:3

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

May 18, 2021

Pars Genome Lab

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Sep 01, 1994

OMIM

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: literature only

- -

Aug 01, 2017

Phosphorus, Inc.

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided

Benign:3

Breakthrough Genomics, Breakthrough Genomics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Sep 11, 2017

Athena Diagnostics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Aug 12, 2024

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Duchenne muscular dystrophy;C0878544:Cardiomyopathy;C0917713:Becker muscular dystrophy;na:Dystrophin deficiency

Benign:1

Aug 09, 2017

Natera, Inc.

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Dilated cardiomyopathy 3B

Benign:1

Apr 27, 2017

Illumina Laboratory Services, Illumina

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -

Cardiovascular phenotype

Benign:1

Oct 23, 2015

Ambry Genetics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.15

BayesDel_addAF

Benign

-0.48

BayesDel_noAF

Benign

-0.40

CADD

Uncertain

DANN

Uncertain

0.99

DEOGEN2

Benign

0.34

.;T;T;T;.;.;T;.;.;T

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Uncertain

0.90

D;.;.;.;.;D;.;D;D;.

MetaRNN

Benign

0.010

T;T;T;T;T;T;T;T;T;T

MetaSVM

Benign

-1.0

PrimateAI

Uncertain

0.50

PROVEAN

Benign

-2.3

N;.;N;N;N;.;D;.;D;N

REVEL

Benign

0.20

Sift

Uncertain

0.0040

D;.;T;T;T;.;D;.;D;T

Sift4G

Benign

0.30

T;T;T;T;T;T;T;T;T;T

Polyphen

0.075, 0.96, 0.0050, 0.98

.;.;B;D;B;.;D;.;.;B

Vest4

0.27, 0.28, 0.27, 0.31, 0.28, 0.17, 0.27, 0.11, 0.28

MPC

0.056

ClinPred

0.045

GERP RS

5.4

gMVP

0.25

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

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