X-32485102-G-C

Variant names:

• chrX-32485102-G-C
• rs863224988
• NM_004006.3:c.2623-3C>G

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM2 PP3 PP5_Very_Strong

The NM_004006.3(DMD):​c.2623-3C>G variant causes a splice region, 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. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★).

• Frequency: Genomes: not found (cov: 22)
• Consequence: DMD NM_004006.3 splice_region, intron
• Scores: Splicing: ADA: 0.9971
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:4
• Conservation: PhyloP100: 2.22

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 11 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF, max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant X-32485102-G-C is Pathogenic according to our data. Variant chrX-32485102-G-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 217186.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-32485102-G-C is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DMD	NM_004006.3	c.2623-3C>G		splice_region_variant, intron_variant	Intron 20 of 78	ENST00000357033.9	NP_003997.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DMD	ENST00000357033.9	c.2623-3C>G		splice_region_variant, intron_variant	Intron 20 of 78	1	NM_004006.3	ENSP00000354923.3

Frequencies

GnomAD3 genomes Cov.: 22

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 22

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:4

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Duchenne muscular dystrophy Pathogenic:2

Feb 02, 2022

Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Likely pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with Duchenne muscular dystrophy (DMD; MIM#310200), Becker muscular dystrophy (BMD; MIM#300376) and X-linked dominant dilated cardiomyopathy, 3B (DCM; MIM#302045). (I) 0108 - This gene is associated with both recessive and dominant disease. DMD and BMD are both associated with X-linked recessive disease, while females who are heterozygous for a pathogenic DMD variant are at increased risk for DCM. (I) 0212 - Non-canonical splice site variant without proven consequence on splicing (no functional evidence available). This variant has been reported to result in the retention of the last two nucleotides in intron 20 and create a new acceptor splice site; however, no specific functional studies have been shown (PMIDs: 19783145, 22182525). (SP) 0253 - This variant is hemizygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0311 - An alternative nucleotide change at the same non-canonical splice site, is present in gnomAD (v2) at a frequency of 0.0000055 (1 heterozygote, 0 homozygotes). (SB) 0508 - In silico predictions for abnormal splicing are inconclusive. (I) 0705 - No comparable splice variants have previous evidence for pathogenicity. (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been reported at least five individuals with Duchenne muscular dystrophy and/or dystrophinopathies (ClinVar; PMIDs: 19783145, 22182525). (SP) 0905 - No published segregation evidence has been identified for this variant. (I) 1010 - Functional evidence for this variant is inconclusive. Using patient fibroblasts and RNA extracted from patient muscle tissue, this variant has been reported to retain the last two nucleotides in intron 20 and create a new splice site, however specific functional studies demonstrating this has not been shown ((PMIDs: 19783145, 22182525). (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -

Sep 12, 2012

Athena Diagnostics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Qualitative or quantitative defects of dystrophin Pathogenic:1

Feb 22, 2021

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

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: DMD c.2623-3C>G alters a conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: Three predict the variant abolishes a 3 acceptor site and creates a new cryptic intronic one. Experimental evidence supports these predictions demonstrating the variant leads to the retention of the last 2 AG nucleotides of intron 20 in the mature dystrophin mRNA (Sedlackova_2009, Adkin_2012). The variant was absent in 183222 control chromosomes (gnomAD). c.2623-3C>G has been reported in the literature in individuals affected with Dystrophinopathies (e.g. Sedlackova_2009, Adkin_2012). These data indicate that the variant may be associated with disease. A ClinVar submitter (evaluation after 2014) cites the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

not provided Pathogenic:1

May 16, 2017

Eurofins Ntd Llc (ga)

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	23
DANN	Benign	0.55

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.77
SpliceAI score (max)		0.98		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.98		Position offset: -1
DS_AL_spliceai		0.93		Position offset: -3

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

Publications

LitVar

Other links and lift over

dbSNP: rs863224988; hg19: chrX-32503219;