rs373448002
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PP3_ModerateBP6_Very_StrongBS2
The NM_004006.3(DMD):c.9790C>T(p.Arg3264Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000232 in 1,207,551 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 9 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R3264Q) has been classified as Likely benign.
Frequency
Consequence
NM_004006.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DMD | NM_004006.3 | c.9790C>T | p.Arg3264Trp | missense_variant | 67/79 | ENST00000357033.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DMD | ENST00000357033.9 | c.9790C>T | p.Arg3264Trp | missense_variant | 67/79 | 1 | NM_004006.3 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00000891 AC: 1AN: 112264Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 34464
GnomAD3 exomes AF: 0.0000109 AC: 2AN: 183339Hom.: 0 AF XY: 0.0000147 AC XY: 1AN XY: 67815
GnomAD4 exome AF: 0.0000247 AC: 27AN: 1095287Hom.: 0 Cov.: 29 AF XY: 0.0000249 AC XY: 9AN XY: 360735
GnomAD4 genome AF: 0.00000891 AC: 1AN: 112264Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 34464
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 18, 2021 | In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 27535533) - |
Duchenne muscular dystrophy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 16, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at