18-31086560-TTAA-TTAATAA
Variant summary
Our verdict is Likely benign. The variant received -6 ACMG points: 2P and 8B. PM2BP6_Very_Strong
The NM_024422.6(DSC2):c.942+13_942+15dupTTA variant causes a 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 intron
NM_024422.6 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.797
Publications
1 publications found
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]
DSC2 Gene-Disease associations (from GenCC):
- arrhythmogenic right ventricular dysplasia 11Inheritance: AD, AR, SD Classification: DEFINITIVE, STRONG, LIMITED Submitted by: G2P, Labcorp Genetics (formerly Invitae), Genomics England PanelApp, Ambry Genetics
- familial isolated arrhythmogenic right ventricular dysplasiaInheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
- colorectal adenomaInheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -6 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant 18-31086560-T-TTAA is Benign according to our data. Variant chr18-31086560-T-TTAA is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 46203.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_024422.6. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| DSC2 | TSL:1 MANE Select | c.942+15_942+16insTTA | intron | N/A | ENSP00000280904.6 | Q02487-1 | |||
| DSC2 | TSL:1 | c.942+15_942+16insTTA | intron | N/A | ENSP00000251081.6 | Q02487-2 | |||
| DSC2 | c.942+15_942+16insTTA | intron | N/A | ENSP00000519010.1 | A0AAQ5BGP6 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD2 exomes AF: 0.999 AC: 251235AN: 251386 AF XY: 1.00 show subpopulations
GnomAD2 exomes
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251235
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251386
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GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome
GnomAD4 genome
Cov.:
32
Alfa
AF:
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Asia WGS
AF:
AC:
3475
AN:
3478
ClinVar
ClinVar submissions
View on ClinVar Significance:Benign/Likely benign
Revision:criteria provided, multiple submitters, no conflicts
Pathogenic
VUS
Benign
Condition
-
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3
not specified (3)
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2
Arrhythmogenic right ventricular dysplasia 11 (2)
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1
Arrhythmogenic right ventricular cardiomyopathy (1)
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1
Cardiovascular phenotype (1)
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1
not provided (1)
Computational scores
Source:
Name
Calibrated prediction
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Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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