rs10502571

chr18-31503053-G-A

Variant summary

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

The NM_001943.5(DSG2):c.45+4757G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.088 in 152,168 control chromosomes in the GnomAD database, including 1,493 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 0.088 (1493 hom., cov: 32)
• Consequence: DSG2 NM_001943.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.241

Genes affected

DSG2 (HGNC:3049): (desmoglein 2) This gene encodes a member of the desmoglein family and cadherin cell adhesion molecule superfamily of proteins. Desmogleins are calcium-binding transmembrane glycoprotein components of desmosomes, cell-cell junctions between epithelial, myocardial, and other cell types. The encoded preproprotein is proteolytically processed to generate the mature glycoprotein. This gene is present in a gene cluster with other desmoglein gene family members on chromosome 18. Mutations in this gene have been associated with arrhythmogenic right ventricular dysplasia, familial, 10. [provided by RefSeq, Jan 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DSG2	NM_001943.5	c.45+4757G>A		intron_variant		ENST00000261590.13
DSG2	XM_047437315.1	c.-528+4757G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DSG2	ENST00000261590.13	c.45+4757G>A		intron_variant		1	NM_001943.5	P1
DSG2	ENST00000585206.1	c.45+4757G>A		intron_variant		2
DSG2	ENST00000682241.2	c.45+4757G>A		intron_variant
DSG2	ENST00000683654.1	c.45+4757G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.0879 AC: 13371 AN: 152050 Hom.: 1498 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0385

Gnomad ASJ AF: 0.00720

Gnomad EAS AF: 0.0306

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0121

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0128

Gnomad OTH AF: 0.0602

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

GnomAD4 genome AF: 0.0880 AC: 13386 AN: 152168 Hom.: 1493 Cov.: 32 AF XY: 0.0873 AC XY: 6497 AN XY: 74402

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.0384

Gnomad4 ASJ AF: 0.00720

Gnomad4 EAS AF: 0.0307

Gnomad4 SAS AF: 0.123

Gnomad4 FIN AF: 0.0121

Gnomad4 NFE AF: 0.0128

Gnomad4 OTH AF: 0.0596

Alfa AF: 0.0345 Hom.: 174

Bravo AF: 0.0954

Asia WGS AF: 0.0960 AC: 335 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.37
Dann	Benign	0.42

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: rs10502571; hg19: chr18-29083016;