rs397517401
Positions:
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM2BP6_Very_Strong
The NM_024422.6(DSC2):c.630+8_630+10delinsTT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: not found (cov: 32)
Consequence
DSC2
NM_024422.6 splice_region, intron
NM_024422.6 splice_region, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.78
Genes affected
DSC2 (HGNC:3036): (desmocollin 2) This gene encodes a member of the desmocollin protein subfamily. Desmocollins, along with desmogleins, are cadherin-like transmembrane glycoproteins that are major components of the desmosome. Desmosomes are cell-cell junctions that help resist shearing forces and are found in high concentrations in cells subject to mechanical stress. This gene is found in a cluster with other desmocollin family members on chromosome 18. Mutations in this gene are associated with arrhythmogenic right ventricular dysplasia-11, and reduced protein expression has been described in several types of cancer. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2015]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP6
?
Variant 18-31089429-TAG-AA is Benign according to our data. Variant chr18-31089429-TAG-AA is described in ClinVar as [Likely_benign]. Clinvar id is 46193.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DSC2 | NM_024422.6 | c.630+8_630+10delinsTT | splice_region_variant, intron_variant | ENST00000280904.11 | |||
DSC2 | NM_001406506.1 | c.201+8_201+10delinsTT | splice_region_variant, intron_variant | ||||
DSC2 | NM_001406507.1 | c.201+8_201+10delinsTT | splice_region_variant, intron_variant | ||||
DSC2 | NM_004949.5 | c.630+8_630+10delinsTT | splice_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DSC2 | ENST00000280904.11 | c.630+8_630+10delinsTT | splice_region_variant, intron_variant | 1 | NM_024422.6 | P1 | |||
DSC2 | ENST00000251081.8 | c.630+8_630+10delinsTT | splice_region_variant, intron_variant | 1 | |||||
DSC2 | ENST00000648081.1 | c.201+8_201+10delinsTT | splice_region_variant, intron_variant | ||||||
DSC2 | ENST00000682357.1 | c.201+8_201+10delinsTT | splice_region_variant, intron_variant |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Apr 04, 2012 | 630+8_630+10delinsTT in intron 5 of DSC2: This variant is not expected to have c linical significance because it is not located within the splice consensus seque nce. 630+8_630+10delinsTT in intron 5 of DSC2 (allele frequency = n/a) - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 10, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at