chr18-31326497-T-C
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_001942.4(DSG1):c.49-84T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.463 in 1,088,920 control chromosomes in the GnomAD database, including 123,677 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.41 ( 14036 hom., cov: 32)
Exomes 𝑓: 0.47 ( 109641 hom. )
Consequence
DSG1
NM_001942.4 intron
NM_001942.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.28
Genes affected
DSG1 (HGNC:3048): (desmoglein 1) This gene encodes a member of the desmoglein protein subfamily. Desmogleins, along with desmocollins, 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 desmoglein family members on chromosome 18. The encoded protein has been identified as a target of auto-antibodies in the autoimmune skin blistering disease pemphigus foliaceus. Disruption of this gene has also been associated with the skin diseases palmoplantar keratoderma and erythroderma. [provided by RefSeq, Feb 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BP6
?
Variant 18-31326497-T-C is Benign according to our data. Variant chr18-31326497-T-C is described in ClinVar as [Benign]. Clinvar id is 1265775.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DSG1 | NM_001942.4 | c.49-84T>C | intron_variant | ENST00000257192.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DSG1 | ENST00000257192.5 | c.49-84T>C | intron_variant | 1 | NM_001942.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.412 AC: 62405AN: 151450Hom.: 14041 Cov.: 32
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GnomAD4 exome AF: 0.471 AC: 441773AN: 937352Hom.: 109641 AF XY: 0.474 AC XY: 229589AN XY: 484368
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GnomAD4 genome ? AF: 0.412 AC: 62419AN: 151568Hom.: 14036 Cov.: 32 AF XY: 0.414 AC XY: 30686AN XY: 74036
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 11, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at