X-32385620-T-TAATTTTAAACCATCAAAGCTCTA

Variant names:

• chrX-32385620-T-TAATTTTAAACCATCAAAGCTCTA
• rs6151281
• NM_004006.3:c.4674+689_4674+690insTAGAGCTTTGATGGTTTAAAATT

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.

The NM_004006.3(DMD):​c.4674+689_4674+690insTAGAGCTTTGATGGTTTAAAATT variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.69 (19289 hom., 20976 hem., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: DMD NM_004006.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0830

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 Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DMD	NM_004006.3	c.4674+689_4674+690insTAGAGCTTTGATGGTTTAAAATT		intron_variant	Intron 33 of 78	ENST00000357033.9	NP_003997.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DMD	ENST00000357033.9	c.4674+689_4674+690insTAGAGCTTTGATGGTTTAAAATT		intron_variant	Intron 33 of 78	1	NM_004006.3	ENSP00000354923.3

Frequencies

GnomAD3 genomes AF: 0.694 AC: 74855 AN: 107789 Hom.: 19288 Cov.: 0 AF XY: 0.683 AC XY: 20937 AN XY: 30657

Gnomad AFR AF: 0.835

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.747

Gnomad ASJ AF: 0.537

Gnomad EAS AF: 0.774

Gnomad SAS AF: 0.714

Gnomad FIN AF: 0.711

Gnomad MID AF: 0.550

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.686

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.694 AC: 74885 AN: 107837 Hom.: 19289 Cov.: 0 AF XY: 0.683 AC XY: 20976 AN XY: 30715

Gnomad4 AFR AF: 0.835

Gnomad4 AMR AF: 0.748

Gnomad4 ASJ AF: 0.537

Gnomad4 EAS AF: 0.774

Gnomad4 SAS AF: 0.709

Gnomad4 FIN AF: 0.711

Gnomad4 NFE AF: 0.608

Gnomad4 OTH AF: 0.679

Alfa AF: 0.429 Hom.: 1292

Asia WGS AF: 0.707 AC: 1779 AN: 2518

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6151281; hg19: chrX-32403737;