rs367702968
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_004006.3(DMD):c.6052C>A(p.Leu2018Ile) variant causes a missense change. The variant allele was found at a frequency of 0.0000431 in 1,207,897 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 15 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. L2018R) 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.6052C>A | p.Leu2018Ile | missense_variant | 42/79 | ENST00000357033.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DMD | ENST00000357033.9 | c.6052C>A | p.Leu2018Ile | missense_variant | 42/79 | 1 | NM_004006.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.000242 AC: 27AN: 111672Hom.: 0 Cov.: 23 AF XY: 0.000206 AC XY: 7AN XY: 34018
GnomAD3 exomes AF: 0.0000329 AC: 6AN: 182281Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67267
GnomAD4 exome AF: 0.0000228 AC: 25AN: 1096172Hom.: 0 Cov.: 30 AF XY: 0.0000221 AC XY: 8AN XY: 362486
GnomAD4 genome ? AF: 0.000242 AC: 27AN: 111725Hom.: 0 Cov.: 23 AF XY: 0.000205 AC XY: 7AN XY: 34081
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Nov 14, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Apr 30, 2021 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 14, 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. - |
Duchenne muscular dystrophy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 29, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at