X-31875367-TGGAAACCTGAAAGGAAA-T

Variant names:

• chrX-31875367-TGGAAACCTGAAAGGAAA-T
• rs1556962571
• NM_004006.3:c.6913-11_6918delTTTCCTTTCAGGTTTCC

Variant summary

Our verdict is Uncertain significance. The variant received 4 ACMG points: 4P and 0B. PVS1_Moderate PP5_Moderate

The NM_004006.3(DMD):​c.6913-11_6918delTTTCCTTTCAGGTTTCC​(p.Val2305_Arg2307del) variant causes a splice acceptor, conservative inframe deletion, splice region, intron change. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Likely pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. V2305V) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 23)
• Consequence: DMD NM_004006.3 splice_acceptor, conservative_inframe_deletion, splice_region, intron
• Clinical Significance: Likely pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 5.94
• Publications: 0 publications found

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

ACMG classification

Our verdict: Uncertain_significance. The variant received 4 ACMG points.

• PVS1: Splicing +-2 bp (donor or acceptor) variant, product NOT destroyed by NMD, known LOF gene, truncates exone, which is 0.016820401 fraction of the gene. No cryptic splice site detected. Exon removal is inframe change.
• PP5: Variant X-31875367-TGGAAACCTGAAAGGAAA-T is Pathogenic according to our data. Variant chrX-31875367-TGGAAACCTGAAAGGAAA-T is described in ClinVar as Likely_pathogenic. ClinVar VariationId is 455926.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004006.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DMD	NM_004006.3	MANE Select	c.6913-11_6918delTTTCCTTTCAGGTTTCC	p.Val2305_Arg2307del	splice_acceptor conservative_inframe_deletion splice_region intron	Exon 48 of 79	NP_003997.2
	DMD	NM_004021.3		c.-468-11_-463delTTTCCTTTCAGGTTTCC		splice_region	Exon 5 of 35	NP_004012.2
	DMD	NM_004022.3		c.-468-11_-463delTTTCCTTTCAGGTTTCC		splice_region	Exon 5 of 34	NP_004013.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DMD	ENST00000357033.9	TSL:1 MANE Select	c.6913-11_6918delTTTCCTTTCAGGTTTCC	p.Val2305_Arg2307del	splice_acceptor conservative_inframe_deletion splice_region intron	Exon 48 of 79	ENSP00000354923.3
	DMD	ENST00000474231.5	TSL:5	c.-468-11_-463delTTTCCTTTCAGGTTTCC		splice_region	Exon 5 of 35	ENSP00000417123.1
	DMD	ENST00000359836.5	TSL:5	c.-468-11_-463delTTTCCTTTCAGGTTTCC		splice_region	Exon 5 of 34	ENSP00000352894.1

Frequencies

GnomAD3 genomes Cov.: 23

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 23

ClinVar

ClinVar submissions as Germline

Significance: Likely pathogenic

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
1	-	-	Duchenne muscular dystrophy (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		5.9

Splicing

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

Other links and lift over

dbSNP: rs1556962571; hg19: chrX-31893484;