X-32697953-T-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_004006.3(DMD):āc.877A>Gā(p.Lys293Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000999 in 1,201,764 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Synonymous variant affecting the same amino acid position (i.e. K293K) has been classified as Likely benign.
Frequency
Consequence
NM_004006.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DMD | NM_004006.3 | c.877A>G | p.Lys293Glu | missense_variant | 9/79 | ENST00000357033.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DMD | ENST00000357033.9 | c.877A>G | p.Lys293Glu | missense_variant | 9/79 | 1 | NM_004006.3 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00000914 AC: 1AN: 109369Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 31743
GnomAD3 exomes AF: 0.0000116 AC: 2AN: 171730Hom.: 0 AF XY: 0.0000173 AC XY: 1AN XY: 57716
GnomAD4 exome AF: 0.0000101 AC: 11AN: 1092395Hom.: 0 Cov.: 30 AF XY: 0.0000112 AC XY: 4AN XY: 358531
GnomAD4 genome AF: 0.00000914 AC: 1AN: 109369Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 31743
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. | Apr 27, 2020 | - - |
Duchenne muscular dystrophy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jun 14, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at