chrX-32362932-T-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2
The NM_004006.3(DMD):c.5181A>T(p.Ile1727=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000143 in 1,208,982 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 74 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).
Frequency
Consequence
NM_004006.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DMD | NM_004006.3 | c.5181A>T | p.Ile1727= | synonymous_variant | 37/79 | ENST00000357033.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DMD | ENST00000357033.9 | c.5181A>T | p.Ile1727= | synonymous_variant | 37/79 | 1 | NM_004006.3 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000387 AC: 43AN: 111207Hom.: 0 Cov.: 22 AF XY: 0.000509 AC XY: 17AN XY: 33381
GnomAD3 exomes AF: 0.000181 AC: 33AN: 181927Hom.: 0 AF XY: 0.000240 AC XY: 16AN XY: 66571
GnomAD4 exome AF: 0.000118 AC: 130AN: 1097717Hom.: 0 Cov.: 31 AF XY: 0.000157 AC XY: 57AN XY: 363139
GnomAD4 genome AF: 0.000386 AC: 43AN: 111265Hom.: 0 Cov.: 22 AF XY: 0.000508 AC XY: 17AN XY: 33449
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:2
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jul 11, 2016 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | May 02, 2018 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2024 | DMD: BP4, BP7, BS2 - |
Duchenne muscular dystrophy Benign:2
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | May 18, 2021 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 27, 2024 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Apr 17, 2019 | The p.Ile1727Ile variant in DMD is classified as benign because it has been identified in 0.05% (14/27930) of Latino chromosomes and 20 hemizygotes by gnomAD (http://gnomad.broadinstitute.org). In addition, it does not alter an amino acid residue, it is not located within the splice consensus sequence, and splice prediction algorithms do not predict a newly created splice site. ACMG/AMP Criteria applied: BA1, BP4, BP7. - |
Duchenne muscular dystrophy;C0878544:Cardiomyopathy;C0917713:Becker muscular dystrophy;na:Dystrophin deficiency Benign:1
Likely benign, no assertion criteria provided | clinical testing | Natera, Inc. | Apr 10, 2018 | - - |
Cardiovascular phenotype Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 03, 2018 | This alteration is classified as 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