rs722576

Variant names:

• chrX-32317045-T-A
• rs722576
• NM_004006.3:c.5923-6769A>T

Your query was ambiguous. Multiple possible variants found:

• chrX-32317045-T-A
• chrX-32317045-T-C
• chrX-32317045-T-G

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 0P and 3B. BP4_Moderate BP6

The NM_004006.3(DMD):​c.5923-6769A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.74 (21349 hom., 23437 hem., cov: 22)
  • Failed GnomAD Quality Control
• Consequence: DMD NM_004006.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.02

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 Likely_benign. Variant got -3 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.35).
• BP6: Variant X-32317045-T-A is Benign according to our data. Variant chrX-32317045-T-A is described in Lovd as [Benign].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DMD	NM_004006.3	c.5923-6769A>T		intron_variant	Intron 41 of 78	ENST00000357033.9	NP_003997.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DMD	ENST00000357033.9	c.5923-6769A>T		intron_variant	Intron 41 of 78	1	NM_004006.3	ENSP00000354923.3

Frequencies

GnomAD3 genomes AF: 0.737 AC: 80700 AN: 109520 Hom.: 21360 Cov.: 22 AF XY: 0.732 AC XY: 23398 AN XY: 31968

Gnomad AFR AF: 0.659

Gnomad AMI AF: 0.628

Gnomad AMR AF: 0.807

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.822

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.767

Gnomad OTH AF: 0.773

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: 0.737 AC: 80713 AN: 109575 Hom.: 21349 Cov.: 22 AF XY: 0.732 AC XY: 23437 AN XY: 32033

Gnomad4 AFR AF: 0.659

Gnomad4 AMR AF: 0.807

Gnomad4 ASJ AF: 0.822

Gnomad4 EAS AF: 0.719

Gnomad4 SAS AF: 0.820

Gnomad4 FIN AF: 0.686

Gnomad4 NFE AF: 0.767

Gnomad4 OTH AF: 0.765

Alfa AF: 0.759 Hom.: 6250

Bravo AF: 0.737

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.35
CADD	Benign	14
DANN	Benign	0.70

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs722576; hg19: chrX-32335162;