6-7567794-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBP6_Very_Strong
The NM_004415.4(DSP):c.1154C>T(p.Ala385Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000551 in 1,613,844 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 (★★). Synonymous variant affecting the same amino acid position (i.e. A385A) has been classified as Likely benign.
Frequency
Consequence
NM_004415.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DSP | NM_004415.4 | c.1154C>T | p.Ala385Val | missense_variant | 10/24 | ENST00000379802.8 | |
DSP | NM_001319034.2 | c.1154C>T | p.Ala385Val | missense_variant | 10/24 | ||
DSP | NM_001008844.3 | c.1154C>T | p.Ala385Val | missense_variant | 10/24 | ||
DSP | NM_001406591.1 | c.1154C>T | p.Ala385Val | missense_variant | 10/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DSP | ENST00000379802.8 | c.1154C>T | p.Ala385Val | missense_variant | 10/24 | 1 | NM_004415.4 | P2 | |
DSP | ENST00000418664.2 | c.1154C>T | p.Ala385Val | missense_variant | 10/24 | 1 | A2 | ||
DSP | ENST00000710359.1 | c.1154C>T | p.Ala385Val | missense_variant | 10/24 | A2 | |||
DSP | ENST00000682228.1 | n.809C>T | non_coding_transcript_exon_variant | 3/3 |
Frequencies
GnomAD3 genomes AF: 0.000263 AC: 40AN: 152054Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000103 AC: 26AN: 251226Hom.: 0 AF XY: 0.0000516 AC XY: 7AN XY: 135778
GnomAD4 exome AF: 0.0000335 AC: 49AN: 1461674Hom.: 0 Cov.: 34 AF XY: 0.0000206 AC XY: 15AN XY: 727144
GnomAD4 genome AF: 0.000263 AC: 40AN: 152170Hom.: 0 Cov.: 32 AF XY: 0.000242 AC XY: 18AN XY: 74388
ClinVar
Submissions by phenotype
Cardiomyopathy Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario | Feb 15, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Oct 23, 2019 | - - |
Arrhythmogenic cardiomyopathy with wooly hair and keratoderma Benign:1
Likely benign, criteria provided, single submitter | clinical testing | All of Us Research Program, National Institutes of Health | Feb 05, 2024 | - - |
Arrhythmogenic right ventricular dysplasia 8;C1854063:Arrhythmogenic cardiomyopathy with wooly hair and keratoderma Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 13, 2024 | - - |
Arrhythmogenic right ventricular cardiomyopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Lethal acantholytic epidermolysis bullosa Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Woolly hair-skin fragility syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 24, 2020 | This variant is associated with the following publications: (PMID: 26220970) - |
Epidermolysis bullosa simplex due to plakophilin deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Cardiovascular phenotype Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 28, 2020 | 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