rs373832446
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_004006.3(DMD):c.8255A>G(p.Tyr2752Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000247 in 1,208,631 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 93 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. Y2752H) has been classified as Uncertain significance.
Frequency
Consequence
NM_004006.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DMD | NM_004006.3 | c.8255A>G | p.Tyr2752Cys | missense_variant | 56/79 | ENST00000357033.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DMD | ENST00000357033.9 | c.8255A>G | p.Tyr2752Cys | missense_variant | 56/79 | 1 | NM_004006.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000151 AC: 17AN: 112350Hom.: 0 Cov.: 23 AF XY: 0.000145 AC XY: 5AN XY: 34500
GnomAD3 exomes AF: 0.000168 AC: 30AN: 178045Hom.: 0 AF XY: 0.0000794 AC XY: 5AN XY: 62971
GnomAD4 exome AF: 0.000256 AC: 281AN: 1096281Hom.: 0 Cov.: 30 AF XY: 0.000243 AC XY: 88AN XY: 361749
GnomAD4 genome ? AF: 0.000151 AC: 17AN: 112350Hom.: 0 Cov.: 23 AF XY: 0.000145 AC XY: 5AN XY: 34500
ClinVar
Submissions by phenotype
not provided Uncertain:2Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Jan 20, 2021 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Aug 10, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 02, 2021 | - - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Sep 26, 2018 | The DMD p.Tyr2752Cys variant (rs373832446), to our knowledge, has not been reported in the medical literature or gene specific databases; however, this variant is also listed in the ClinVar database with conflicting interpretations (Variation ID: 94797). This variant is found in the general population with an allele frequency in non-Finnish Europeans of 0.03% (28/87,438 alleles; including 5 hemizygotes) in the Genome Aggregation Database. The tyrosine at codon 2752 is highly conserved and computational analyses (SIFT, PolyPhen-2) predict that this variant is deleterious. Thus, based on the available information, the clinical significance of this variant is uncertain. - |
Duchenne muscular dystrophy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 12, 2022 | 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