rs200928985
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_004006.3(DMD):c.9352G>T(p.Ala3118Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000348 in 1,207,203 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 15 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. A3118T) has been classified as Likely benign.
Frequency
Consequence
NM_004006.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DMD | NM_004006.3 | c.9352G>T | p.Ala3118Ser | missense_variant | 64/79 | ENST00000357033.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DMD | ENST00000357033.9 | c.9352G>T | p.Ala3118Ser | missense_variant | 64/79 | 1 | NM_004006.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000357 AC: 4AN: 112027Hom.: 0 Cov.: 23 AF XY: 0.0000293 AC XY: 1AN XY: 34187
GnomAD3 exomes AF: 0.0000436 AC: 8AN: 183500Hom.: 0 AF XY: 0.0000294 AC XY: 2AN XY: 67936
GnomAD4 exome AF: 0.0000347 AC: 38AN: 1095176Hom.: 0 Cov.: 29 AF XY: 0.0000388 AC XY: 14AN XY: 360614
GnomAD4 genome ? AF: 0.0000357 AC: 4AN: 112027Hom.: 0 Cov.: 23 AF XY: 0.0000293 AC XY: 1AN XY: 34187
ClinVar
Submissions by phenotype
Duchenne muscular dystrophy Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Pars Genome Lab | May 18, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 06, 2023 | - - |
Duchenne muscular dystrophy;C0917713:Becker muscular dystrophy;C3668940:Dilated cardiomyopathy 3B Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 31, 2018 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Jan 03, 2020 | - - |
Primary familial dilated cardiomyopathy Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute | Jul 18, 2017 | - - |
Cardiovascular phenotype Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 26, 2021 | The p.A3118S variant (also known as c.9352G>T), located in coding exon 64 of the DMD gene, results from a G to T substitution at nucleotide position 9352. The alanine at codon 3118 is replaced by serine, an amino acid with similar properties. This amino acid position is highly conserved in available vertebrate species. Based on data from gnomAD, the T allele has an overall frequency of 0.004% (8/183500) total alleles studied, with 2 hemizygote(s) observed. The highest observed frequency was 0.01% (8/81942) of non-Finnish European alleles. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at