rs201262489
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_StrongBP6BS2
The NM_004006.3(DMD):c.7130C>T(p.Pro2377Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000446 in 1,209,499 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 24 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). Synonymous variant affecting the same amino acid position (i.e. P2377P) 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 -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DMD | NM_004006.3 | c.7130C>T | p.Pro2377Leu | missense_variant | 49/79 | ENST00000357033.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DMD | ENST00000357033.9 | c.7130C>T | p.Pro2377Leu | missense_variant | 49/79 | 1 | NM_004006.3 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000716 AC: 8AN: 111781Hom.: 0 Cov.: 23 AF XY: 0.000118 AC XY: 4AN XY: 33987
GnomAD3 exomes AF: 0.0000600 AC: 11AN: 183331Hom.: 0 AF XY: 0.0000737 AC XY: 5AN XY: 67813
GnomAD4 exome AF: 0.0000419 AC: 46AN: 1097663Hom.: 0 Cov.: 30 AF XY: 0.0000551 AC XY: 20AN XY: 363061
GnomAD4 genome AF: 0.0000715 AC: 8AN: 111836Hom.: 0 Cov.: 23 AF XY: 0.000117 AC XY: 4AN XY: 34052
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Aug 08, 2016 | - - |
Duchenne muscular dystrophy;C0878544:Cardiomyopathy;C0917713:Becker muscular dystrophy;na:Dystrophin deficiency Benign:1
Likely benign, no assertion criteria provided | clinical testing | Natera, Inc. | Jun 01, 2018 | - - |
Duchenne muscular dystrophy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 13, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at