rs745766977
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PP3BP6BS2
The NM_004006.3(DMD):āc.10211A>Gā(p.Asp3404Gly) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000207 in 1,205,433 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 Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D3404E) has been classified as Likely benign.
Frequency
Consequence
NM_004006.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DMD | NM_004006.3 | c.10211A>G | p.Asp3404Gly | missense_variant | 70/79 | ENST00000357033.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DMD | ENST00000357033.9 | c.10211A>G | p.Asp3404Gly | missense_variant | 70/79 | 1 | NM_004006.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000178 AC: 2AN: 112198Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34400
GnomAD3 exomes AF: 0.0000110 AC: 2AN: 182220Hom.: 0 AF XY: 0.0000149 AC XY: 1AN XY: 66934
GnomAD4 exome AF: 0.0000210 AC: 23AN: 1093235Hom.: 0 Cov.: 30 AF XY: 0.0000250 AC XY: 9AN XY: 359403
GnomAD4 genome ? AF: 0.0000178 AC: 2AN: 112198Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34400
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Jul 12, 2023 | - - |
Dystrophin deficiency Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Sep 16, 2020 | - - |
Cardiovascular phenotype Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 29, 2024 | The p.D3404G variant (also known as c.10211A>G), located in coding exon 70 of the DMD gene, results from an A to G substitution at nucleotide position 10211. The aspartic acid at codon 3404 is replaced by glycine, an amino acid with similar properties. Based on data from gnomAD, the G allele has an overall frequency of 0.001% (2/182220) total alleles studied, with 1 hemizygote observed. The highest observed frequency was 0.008% (1/13150) of African/African-American alleles. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Duchenne muscular dystrophy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 10, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at