chr18-31322359-A-G

Position:

• chr18-31322359-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001942.4(DSG1):​c.48+4011A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0642 in 152,320 control chromosomes in the GnomAD database, including 434 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.064 (434 hom., cov: 33)
• Consequence: DSG1 NM_001942.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.153

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.125 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DSG1	NM_001942.4	c.48+4011A>G		intron_variant		ENST00000257192.5	NP_001933.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DSG1	ENST00000257192.5	c.48+4011A>G		intron_variant		1	NM_001942.4	ENSP00000257192.4

Frequencies

GnomAD3 genomes AF: 0.0643 AC: 9780 AN: 152202 Hom.: 434 Cov.: 33

Gnomad AFR AF: 0.106

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0681

Gnomad ASJ AF: 0.0211

Gnomad EAS AF: 0.0379

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.0623

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0389

Gnomad OTH AF: 0.0607

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0642 AC: 9781 AN: 152320 Hom.: 434 Cov.: 33 AF XY: 0.0662 AC XY: 4929 AN XY: 74498

Gnomad4 AFR AF: 0.105

Gnomad4 AMR AF: 0.0678

Gnomad4 ASJ AF: 0.0211

Gnomad4 EAS AF: 0.0382

Gnomad4 SAS AF: 0.134

Gnomad4 FIN AF: 0.0623

Gnomad4 NFE AF: 0.0389

Gnomad4 OTH AF: 0.0601

Alfa AF: 0.0444 Hom.: 371

Bravo AF: 0.0659

Asia WGS AF: 0.0850 AC: 297 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.2
DANN	Benign	0.47

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7236477; hg19: chr18-28902322;