Submissions for variant NM_004006.3(DMD):c.7542+13A>G

gnomAD frequency: 0.00407  dbSNP: rs72466585

Total submissions: 14

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Eurofins Ntd Llc (ga)	RCV000150062	SCV000112662	benign	not specified	2018-02-13	criteria provided, single submitter	clinical testing
GeneDx	RCV000150062	SCV000168139	benign	not specified	2014-04-19	criteria provided, single submitter	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.
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000150062	SCV000268969	benign	not specified	2015-01-13	criteria provided, single submitter	clinical testing	c.7542+13A>G in intron 51 of DMD: This variant is not expected to have clinical significance because it is not located within the conserved splice consensus seq uence. It has been identified in 0.8% (51/6728) of European American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http://evs.gs.wa shington.edu/EVS; dbSNP rs72466585).
PreventionGenetics, part of Exact Sciences	RCV000150062	SCV000309942	benign	not specified		criteria provided, single submitter	clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV001529274	SCV001159453	benign	not provided	2020-07-10	criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV001169692	SCV001332452	likely benign	Dilated cardiomyopathy 3B	2018-01-12	criteria provided, single submitter	clinical testing	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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000150062	SCV001338963	benign	not specified	2020-03-12	criteria provided, single submitter	clinical testing	Variant summary: DMD c.7542+13A>G 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. 4/4 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 0.0038 in 181738 control chromosomes in the gnomAD database, including 1 homozygote and 271 hemizygotes. The observed variant frequency is at least 348-fold of the estimated maximal expected allele frequency for a pathogenic variant in DMD causing Dystrophinopathies phenotype, strongly suggesting that the variant is benign. Three ClinVar submitters (evaluation after 2014) cite the variant as benign. Based on the evidence outlined above, the variant was classified as benign.
Labcorp Genetics (formerly Invitae), Labcorp	RCV001511001	SCV001718174	benign	Duchenne muscular dystrophy	2025-02-03	criteria provided, single submitter	clinical testing
Fulgent Genetics, Fulgent Genetics	RCV002483143	SCV002800290	likely benign	Becker muscular dystrophy; Duchenne muscular dystrophy; Dilated cardiomyopathy 3B	2021-07-27	criteria provided, single submitter	clinical testing
Breakthrough Genomics, Breakthrough Genomics	RCV001529274	SCV005209177	likely benign	not provided		criteria provided, single submitter	not provided
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	RCV001529274	SCV001742444	likely benign	not provided		no assertion criteria provided	clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht	RCV000150062	SCV001932181	benign	not specified		no assertion criteria provided	clinical testing
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	RCV000150062	SCV002035893	benign	not specified		no assertion criteria provided	clinical testing
Natera, Inc.	RCV001831871	SCV002087756	benign	Becker muscular dystrophy; Duchenne muscular dystrophy; Cardiomyopathy; Dystrophin deficiency	2018-04-11	no assertion criteria provided	clinical testing