18-31068085-T-C
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 3P and 12B. PM2PP3BP6_Very_StrongBS1
The NM_024422.6(DSC2):āc.2636A>Gā(p.Asp879Gly) variant causes a missense change. The variant allele was found at a frequency of 0.000124 in 1,614,018 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. D879D) has been classified as Likely benign.
Frequency
Consequence
NM_024422.6 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 |
---|---|---|---|---|---|---|---|
DSC2 | NM_024422.6 | c.2636A>G | p.Asp879Gly | missense_variant | 16/16 | ENST00000280904.11 | |
DSC2 | NM_001406506.1 | c.2207A>G | p.Asp736Gly | missense_variant | 16/16 | ||
DSC2 | NM_001406507.1 | c.*138A>G | 3_prime_UTR_variant | 17/17 | |||
DSC2 | NM_004949.5 | c.*138A>G | 3_prime_UTR_variant | 17/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DSC2 | ENST00000280904.11 | c.2636A>G | p.Asp879Gly | missense_variant | 16/16 | 1 | NM_024422.6 | P1 | |
DSC2 | ENST00000251081.8 | c.*138A>G | 3_prime_UTR_variant | 17/17 | 1 | ||||
DSC2 | ENST00000648081.1 | c.2207A>G | p.Asp736Gly | missense_variant | 17/17 | ||||
DSC2 | ENST00000682357.1 | c.2207A>G | p.Asp736Gly | missense_variant | 16/16 |
Frequencies
GnomAD3 genomes AF: 0.000828 AC: 126AN: 152112Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000219 AC: 55AN: 251304Hom.: 0 AF XY: 0.0000957 AC XY: 13AN XY: 135838
GnomAD4 exome AF: 0.0000520 AC: 76AN: 1461788Hom.: 0 Cov.: 31 AF XY: 0.0000371 AC XY: 27AN XY: 727188
GnomAD4 genome AF: 0.000815 AC: 124AN: 152230Hom.: 0 Cov.: 32 AF XY: 0.000752 AC XY: 56AN XY: 74428
ClinVar
Submissions by phenotype
not specified Benign:3
Benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Mar 25, 2021 | Variant summary: DSC2 c.2636A>G (p.Asp879Gly) results in a non-conservative amino acid change located in the Cadherin, cytoplasmic domain (IPR000233) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00022 in 252158 control chromosomes. The observed variant frequency is approximately 22 fold of the estimated maximal expected allele frequency for a pathogenic variant in DSC2 causing Arrhythmia phenotype (1e-05), strongly suggesting that the variant is benign. To our knowledge, no occurrence of c.2636A>G in individuals affected with Arrhythmia and no experimental evidence demonstrating its impact on protein function have been reported. Five clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and a majority consensus of likely benign (n=4). Based on the evidence outlined above, the variant was classified as benign. - |
Benign, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | May 16, 2015 | p.Asp879Gly in exon 16 of DSC2: This variant is not expected to have clinical si gnificance because it has been identified in 0.3% (35/10398) of African chromoso mes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; d bSNP rs143342988). - |
not provided Benign:3
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 16, 2020 | This variant is associated with the following publications: (PMID: 21636032, 25516398, 29802319) - |
Arrhythmogenic right ventricular dysplasia 11 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 28, 2024 | - - |
Cardiomyopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Dec 02, 2018 | - - |
DSC2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | May 21, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 21, 2019 | 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. - |
Familial isolated arrhythmogenic right ventricular dysplasia Benign:1
Likely benign, criteria provided, single submitter | clinical testing | All of Us Research Program, National Institutes of Health | Feb 05, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at