rs143184877

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_004006.3(DMD):​c.3970C>T​(p.Arg1324Cys) variant causes a missense change. The variant allele was found at a frequency of 0.000368 in 1,209,433 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 117 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1324H) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.0019 ( 0 hom., 52 hem., cov: 23)
Exomes 𝑓: 0.00022 ( 0 hom. 65 hem. )

Consequence

DMD
NM_004006.3 missense

Scores

5
5
6

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:15

Conservation

PhyloP100: 5.30

Publications

3 publications found
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 Gene-Disease associations (from GenCC):
  • Becker muscular dystrophy
    Inheritance: XL Classification: DEFINITIVE, SUPPORTIVE Submitted by: Ambry Genetics, Orphanet
  • dilated cardiomyopathy 3B
    Inheritance: XL Classification: DEFINITIVE Submitted by: Ambry Genetics
  • Duchenne and Becker muscular dystrophy
    Inheritance: XL Classification: DEFINITIVE Submitted by: Myriad Women’s Health
  • Duchenne muscular dystrophy
    Inheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), G2P, Orphanet
  • progressive muscular dystrophy
    Inheritance: XL Classification: DEFINITIVE Submitted by: ClinGen
  • familial isolated dilated cardiomyopathy
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • non-syndromic X-linked intellectual disability
    Inheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet
  • symptomatic form of muscular dystrophy of Duchenne and Becker in female carriers
    Inheritance: XL Classification: SUPPORTIVE Submitted by: Orphanet

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.02620092).
BP6
Variant X-32438342-G-A is Benign according to our data. Variant chrX-32438342-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 94608.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00186 (208/111658) while in subpopulation AFR AF = 0.00659 (203/30781). AF 95% confidence interval is 0.00585. There are 0 homozygotes in GnomAd4. There are 52 alleles in the male GnomAd4 subpopulation. Median coverage is 23. This position passed quality control check.
BS2
High AC in GnomAd4 at 208 XL,AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DMDNM_004006.3 linkc.3970C>T p.Arg1324Cys missense_variant Exon 29 of 79 ENST00000357033.9 NP_003997.2 P11532

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DMDENST00000357033.9 linkc.3970C>T p.Arg1324Cys missense_variant Exon 29 of 79 1 NM_004006.3 ENSP00000354923.3 A0A075B6G3

Frequencies

GnomAD3 genomes
AF:
0.00185
AC:
207
AN:
111606
Hom.:
0
Cov.:
23
show subpopulations
Gnomad AFR
AF:
0.00658
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000953
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:
0.0000377
Gnomad OTH
AF:
0.00132
GnomAD2 exomes
AF:
0.000558
AC:
102
AN:
182953
AF XY:
0.000251
show subpopulations
Gnomad AFR exome
AF:
0.00715
Gnomad AMR exome
AF:
0.0000365
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000490
Gnomad OTH exome
AF:
0.000665
GnomAD4 exome
AF:
0.000216
AC:
237
AN:
1097775
Hom.:
0
Cov.:
30
AF XY:
0.000179
AC XY:
65
AN XY:
363219
show subpopulations
African (AFR)
AF:
0.00758
AC:
200
AN:
26390
American (AMR)
AF:
0.0000284
AC:
1
AN:
35201
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
19379
East Asian (EAS)
AF:
0.00
AC:
0
AN:
30157
South Asian (SAS)
AF:
0.00
AC:
0
AN:
54141
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
40512
Middle Eastern (MID)
AF:
0.00363
AC:
15
AN:
4135
European-Non Finnish (NFE)
AF:
0.00000356
AC:
3
AN:
841785
Other (OTH)
AF:
0.000391
AC:
18
AN:
46075
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.486
Heterozygous variant carriers
0
10
21
31
42
52
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Exome Hom
Variant carriers
0
10
20
30
40
50
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.00186
AC:
208
AN:
111658
Hom.:
0
Cov.:
23
AF XY:
0.00153
AC XY:
52
AN XY:
33886
show subpopulations
African (AFR)
AF:
0.00659
AC:
203
AN:
30781
American (AMR)
AF:
0.0000952
AC:
1
AN:
10503
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
2628
East Asian (EAS)
AF:
0.00
AC:
0
AN:
3541
South Asian (SAS)
AF:
0.00
AC:
0
AN:
2663
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
5999
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
216
European-Non Finnish (NFE)
AF:
0.0000377
AC:
2
AN:
53110
Other (OTH)
AF:
0.00131
AC:
2
AN:
1531
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.515
Heterozygous variant carriers
0
9
18
28
37
46
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
4
8
12
16
20
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.000316
Hom.:
12
Bravo
AF:
0.00216
ESP6500AA
AF:
0.00809
AC:
31
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.000667
AC:
81

ClinVar

Significance: Benign/Likely benign
Submissions summary: Benign:15
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not specified Benign:7
Jan 21, 2020
Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

-
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center
Significance:Benign
Review Status:no assertion criteria provided
Collection Method:clinical testing

- -

Oct 22, 2015
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

p.Arg1324Cys in exon 29 of DMD: This variant is not expected to have clinical si gnificance because it has been identified in 0.8% (64/8493) of African chromosom es by the Exome Aggregation Consortium, including 8 hemizygous individuals (ExAC , http://exac.broadinstitute.org; rs143184877). -

Mar 31, 2017
Athena Diagnostics
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Apr 11, 2015
Eurofins Ntd Llc (ga)
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Jan 06, 2017
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. -

Feb 18, 2022
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

not provided Benign:3
Dec 14, 2023
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

-
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen
Significance:Likely benign
Review Status:no assertion criteria provided
Collection Method:clinical testing

- -

-
Breakthrough Genomics, Breakthrough Genomics
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:not provided

- -

Duchenne muscular dystrophy Benign:2
Jan 30, 2025
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

May 28, 2019
Mendelics
Significance:Likely 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 02, 2019
Natera, Inc.
Significance:Benign
Review Status:no assertion criteria provided
Collection Method:clinical testing

- -

Cardiomyopathy Benign:1
May 23, 2018
Center for Advanced Laboratory Medicine, UC San Diego Health, University of California San Diego
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

- -

Cardiovascular phenotype Benign:1
Jun 29, 2018
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
0.23
BayesDel_addAF
Benign
-0.075
T
BayesDel_noAF
Uncertain
0.12
CADD
Pathogenic
28
DANN
Pathogenic
1.0
DEOGEN2
Benign
0.41
.;T;.;.
FATHMM_MKL
Uncertain
0.96
D
LIST_S2
Pathogenic
0.98
D;.;D;D
M_CAP
Pathogenic
0.91
D
MetaRNN
Benign
0.026
T;T;T;T
MetaSVM
Benign
-0.96
T
PhyloP100
5.3
PrimateAI
Uncertain
0.69
T
PROVEAN
Pathogenic
-4.8
.;D;.;D
REVEL
Uncertain
0.40
Sift
Uncertain
0.0010
.;D;.;D
Sift4G
Pathogenic
0.0
D;D;D;D
Polyphen
1.0
.;D;.;.
Vest4
0.73
MVP
0.92
MPC
0.12
ClinPred
0.088
T
GERP RS
5.8
gMVP
0.33
Mutation Taster
=94/6
polymorphism

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs143184877; hg19: chrX-32456459; COSMIC: COSV63734343; API