rs139318945
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_ModerateBP6_ModerateBS2_Supporting
The NM_004006.3(DMD):c.4201G>A(p.Val1401Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000149 in 1,209,502 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 11 hemizygotes in GnomAD. In-silico tool predicts a benign 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. V1401A) has been classified as Uncertain significance.
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.4201G>A | p.Val1401Met | missense_variant | 30/79 | ENST00000357033.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DMD | ENST00000357033.9 | c.4201G>A | p.Val1401Met | missense_variant | 30/79 | 1 | NM_004006.3 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000179 AC: 2AN: 111524Hom.: 0 Cov.: 22 AF XY: 0.0000593 AC XY: 2AN XY: 33728
GnomAD3 exomes AF: 0.0000109 AC: 2AN: 182970Hom.: 0 AF XY: 0.0000148 AC XY: 1AN XY: 67626
GnomAD4 exome AF: 0.0000146 AC: 16AN: 1097978Hom.: 0 Cov.: 31 AF XY: 0.0000248 AC XY: 9AN XY: 363412
GnomAD4 genome AF: 0.0000179 AC: 2AN: 111524Hom.: 0 Cov.: 22 AF XY: 0.0000593 AC XY: 2AN XY: 33728
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. | May 11, 2020 | - - |
Duchenne muscular dystrophy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 15, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at