rs398124091

Variant names:

• chrX-31261663-T-C
• rs398124091
• NM_004006.3:c.9225-647A>G

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM2 PP5_Very_Strong

The NM_004006.3(DMD):​c.9225-647A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency: Genomes: not found (cov: 23)
• Consequence: DMD NM_004006.3 intron
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:5
• Conservation: PhyloP100: 0.704

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]

ACMG classification

Verdict is Pathogenic. Variant got 10 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant X-31261663-T-C is Pathogenic according to our data. Variant chrX-31261663-T-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 94837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-31261663-T-C is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DMD	NM_004006.3	c.9225-647A>G		intron_variant	Intron 62 of 78	ENST00000357033.9	NP_003997.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DMD	ENST00000357033.9	c.9225-647A>G		intron_variant	Intron 62 of 78	1	NM_004006.3	ENSP00000354923.3

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 23

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:5

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Qualitative or quantitative defects of dystrophin Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Feb 13, 2019	The DMD c.9225-647A>G variant is an intronic variant that has been reported in a hemizygous state in two unrelated individuals with Becker muscular dystrophy, one of whom also exhibited intellectual disability (Daoud et al. 2009; Juan-Mateu et al. 2013). A third individual with Becker muscular dystrophy and intellectual disability was reported to have an A>G nucleotide change in intron 62 that led to aberrant splicing and out-of-frame insertion of 67 nucleotides; however, the variant identified could not be confirmed as c.9225-647A>G (Béroud et al. 2004). In two of these reported cases, the variant was shown to have been inherited from the mother. The c.9225-647A>G variant was absent from the X chromosomes of 1200 normal controls and is absent from the Genome Aggregation Database in a region of adequate coverage for genomes. This region is not covered in exome sequencing. Multiple in silico tools predict this nucleotide change affects splicing, and RT-PCR analysis of RNA isolated from all affected patients has demonstrated that the variant results in aberrant use of a cryptic splice site, out-of-frame pseudoexon inclusion, and a prematurely truncated transcript. Semi-quantitative analysis suggested the abnormal transcript dominated expression over the full-length form, consistent with reduced dystrophin protein expression observed in patient muscle biopsy. Based on the collective evidence, the c.9225-647A>G variant is classified as likely pathogenic for dystrophinopathy. -
Pathogenic, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Aug 10, 2022	Variant summary: DMD c.9225-647A>G is located deep within intron 62, far from canonical splice sites. However, several computational tools predict a significant impact on normal splicing: Four predict the variant strengthens a cryptic 5' donor site. Several publications have given experimental evidence confirming that this variant affects mRNA splicing, which results in a frameshift caused by inclusion of a 67nt pseudoexon (e.g. Daoud_2009, Juan-Mateu_2013). The variant was absent in 21957 control chromosomes (gnomAD), and c.9225-647A>G has been reported in the literature in individuals affected with Duchenne Muscular Dystrophy, and Becker's Muscular Dystrophy with some reports of cognitive impairment (e.g.Deburgrave_2007, Daoud_2009, Juan-Mateu_2013, Yun_2021, Waldrop_2022). These data indicate that the variant is likely to be associated with disease. Western blot analysis of patient muscle biopsies have shown that the variant causes weak/trace levels of the Dystrophin protein, including complete loss of one specific DMD product, Dp71 (Daoud_2009). Four ClinVar submitters have assessed the variant since 2014: all classified the variant as likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Apr 29, 2014	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jun 11, 2024	Published functional studies demonstrate a damaging effect, as RT-PCR of patient muscle shows the variant causes a cryptic 5' splice site activation, leading to an abnormal transcript in the presence of residual wild type transcript (PMID: 19602481, 23536893); No data available from control populations to assess the frequency of this variant; This variant is associated with the following publications: (PMID: 23536893, 14659407, 19602481, 17041906, 32176650, Kumaraku2022[Article], 19367636, 28597072, 35165973, 34297739) -

Duchenne muscular dystrophy Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Mar 16, 2024

This sequence change falls in intron 62 of the DMD gene. It does not directly change the encoded amino acid sequence of the DMD protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or disrupted protein product. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the gnomAD database. This variant has been observed in individual(s) with Becker muscular dystrophy (PMID: 14659407, 19602481, 23536893, 34297739; Invitae). ClinVar contains an entry for this variant (Variation ID: 94837). Studies have shown that this variant results in activation of a cryptic splice site and introduces a premature termination codon (PMID: 14659407, 19602481, 23536893). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Uncertain	24
DANN	Benign	0.50

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.74		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.74		Position offset: 0

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

Publications

LitVar

Other links and lift over

dbSNP: rs398124091; hg19: chrX-31279780;