Variant rs255052 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_022355.4(DPEP2):c.732+23C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 1,614,002 control chromosomes in the GnomAD database, including 19,484 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 0.17 ( 2328 hom., cov: 32)

Exomes 𝑓: 0.15 ( 17156 hom. )

Consequence

DPEP2
NM_022355.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.373

Variant links:

Genes affected

DPEP2 (HGNC:23028): (dipeptidase 2) DPEP2 belongs to the membrane-bound dipeptidase (EC 3.4.13.19) family. These enzymes hydrolyze a variety of dipeptides, including leukotriene D4, the beta-lactam ring of some antibiotics, and cystinyl-bis-glycine (cys-bis-gly) formed during glutathione degradation (Habib et al., 2003 [PubMed 12738806]).[supplied by OMIM, Mar 2008]

DPEP2 links:

DUS2 (HGNC:26014): (dihydrouridine synthase 2) This gene encodes a cytoplasmic protein that catalyzes the conversion of uridine residues to dihydrouridine in the D-loop of tRNA. The resulting modified bases confer enhanced regional flexibility to tRNA. The encoded protein may increase the rate of translation by inhibiting an interferon-induced protein kinase. This gene has been implicated in pulmonary carcinogenesis. Alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, Nov 2012]

DUS2 links:

DPEP2 (HGNC:):

DPEP2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.214 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DPEP2	NM_022355.4 linkuse as main transcript	c.732+23C>T		intron_variant		ENST00000393847.6	NP_071750.1	Q9H4A9-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DPEP2	ENST00000393847.6 linkuse as main transcript	c.732+23C>T		intron_variant		1	NM_022355.4	ENSP00000377430.1		Q9H4A9-1

Frequencies

GnomAD3 genomes

AF:

0.171

AC:

26015

AN:

152106

Hom.:

2329

Cov.:

show subpopulations

Gnomad AFR

AF:

0.218

Gnomad AMI

AF:

0.219

Gnomad AMR

AF:

0.157

Gnomad ASJ

AF:

0.164

Gnomad EAS

AF:

0.109

Gnomad SAS

AF:

0.199

Gnomad FIN

AF:

0.195

Gnomad MID

AF:

0.120

Gnomad NFE

AF:

0.145

Gnomad OTH

AF:

0.161

GnomAD3 exomes

AF:

0.166

AC:

41626

AN:

251320

Hom.:

3669

AF XY:

0.165

AC XY:

22372

AN XY:

135826

show subpopulations

Gnomad AFR exome

AF:

0.226

Gnomad AMR exome

AF:

0.166

Gnomad ASJ exome

AF:

0.161

Gnomad EAS exome

AF:

0.113

Gnomad SAS exome

AF:

0.210

Gnomad FIN exome

AF:

0.191

Gnomad NFE exome

AF:

0.149

Gnomad OTH exome

AF:

0.162

GnomAD4 exome

AF:

0.150

AC:

219126

AN:

1461778

Hom.:

17156

Cov.:

AF XY:

0.151

AC XY:

110058

AN XY:

727194

show subpopulations

Gnomad4 AFR exome

AF:

0.209

Gnomad4 AMR exome

AF:

0.169

Gnomad4 ASJ exome

AF:

0.162

Gnomad4 EAS exome

AF:

0.130

Gnomad4 SAS exome

AF:

0.204

Gnomad4 FIN exome

AF:

0.186

Gnomad4 NFE exome

AF:

0.142

Gnomad4 OTH exome

AF:

0.146

GnomAD4 genome

AF:

0.171

AC:

26024

AN:

152224

Hom.:

2328

Cov.:

AF XY:

0.174

AC XY:

12960

AN XY:

74440

show subpopulations

Gnomad4 AFR

AF:

0.218

Gnomad4 AMR

AF:

0.156

Gnomad4 ASJ

AF:

0.164

Gnomad4 EAS

AF:

0.109

Gnomad4 SAS

AF:

0.199

Gnomad4 FIN

AF:

0.195

Gnomad4 NFE

AF:

0.145

Gnomad4 OTH

AF:

0.165

Alfa

AF:

0.152

Hom.:

3142

Bravo

AF:

0.170

Asia WGS

AF:

0.192

AC:

671

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

2.1

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over