rs369583884
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_004006.3(DMD):c.7597G>A(p.Ala2533Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000256 in 1,209,585 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 8 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A2533V) has been classified as Uncertain significance.
Frequency
Consequence
NM_004006.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DMD | NM_004006.3 | c.7597G>A | p.Ala2533Thr | missense_variant | 52/79 | ENST00000357033.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DMD | ENST00000357033.9 | c.7597G>A | p.Ala2533Thr | missense_variant | 52/79 | 1 | NM_004006.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.00000896 AC: 1AN: 111546Hom.: 0 Cov.: 23 AF XY: 0.0000297 AC XY: 1AN XY: 33726
GnomAD3 exomes AF: 0.0000272 AC: 5AN: 183506Hom.: 0 AF XY: 0.0000147 AC XY: 1AN XY: 67938
GnomAD4 exome AF: 0.0000273 AC: 30AN: 1098039Hom.: 0 Cov.: 30 AF XY: 0.0000193 AC XY: 7AN XY: 363409
GnomAD4 genome ? AF: 0.00000896 AC: 1AN: 111546Hom.: 0 Cov.: 23 AF XY: 0.0000297 AC XY: 1AN XY: 33726
ClinVar
Submissions by phenotype
Duchenne muscular dystrophy;C0878544:Cardiomyopathy;C0917713:Becker muscular dystrophy;na:Dystrophin deficiency Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Oct 06, 2018 | - - |
Cardiovascular phenotype Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 12, 2024 | The p.A2533T variant (also known as c.7597G>A), located in coding exon 52 of the DMD gene, results from a G to A substitution at nucleotide position 7597. The alanine at codon 2533 is replaced by threonine, an amino acid with similar properties. Based on data from gnomAD, the A allele has an overall frequency of 0.0027% (5/183506) total alleles studied, with 1 hemizygote(s) observed. The highest observed frequency was 0.0221% (1/4533) of 'Other' alleles. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Based on the available evidence, the clinical significance of this alteration remains unclear. - |
Duchenne muscular dystrophy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 24, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at