Variant rs17574 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP7BA1

The NM_001935.4(DPP4):c.24T>C(p.Leu8=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 1,613,416 control chromosomes in the GnomAD database, including 89,960 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 0.28 ( 6556 hom., cov: 32)

Exomes 𝑓: 0.33 ( 83404 hom. )

Consequence

DPP4
NM_001935.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.179

Variant links:

Genes affected

DPP4 (HGNC:3009): (dipeptidyl peptidase 4) The DPP4 gene encodes dipeptidyl peptidase 4, which is identical to adenosine deaminase complexing protein-2, and to the T-cell activation antigen CD26. It is an intrinsic type II transmembrane glycoprotein and a serine exopeptidase that cleaves X-proline dipeptides from the N-terminus of polypeptides. Dipeptidyl peptidase 4 is highly involved in glucose and insulin metabolism, as well as in immune regulation. This protein was shown to be a functional receptor for Middle East respiratory syndrome coronavirus (MERS-CoV), and protein modeling suggests that it may play a similar role with SARS-CoV-2, the virus responsible for COVID-19. [provided by RefSeq, Apr 2020]

DPP4 links:

DPP4-DT (HGNC:40191): (DPP4 divergent transcript)

DPP4-DT links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.36).

BP7

Synonymous conserved (PhyloP=0.179 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DPP4	NM_001935.4 linkuse as main transcript	c.24T>C	p.Leu8=	synonymous_variant	2/26	ENST00000360534.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DPP4	ENST00000360534.8 linkuse as main transcript	c.24T>C	p.Leu8=	synonymous_variant	2/26	1	NM_001935.4	P3
DPP4-DT	ENST00000693081.1 linkuse as main transcript	n.43A>G		non_coding_transcript_exon_variant	1/4

Frequencies

GnomAD3 genomes

AF:

0.283

AC:

42947

AN:

152012

Hom.:

6553

Cov.:

show subpopulations

Gnomad AFR

AF:

0.242

Gnomad AMI

AF:

0.284

Gnomad AMR

AF:

0.236

Gnomad ASJ

AF:

0.315

Gnomad EAS

AF:

0.0444

Gnomad SAS

AF:

0.298

Gnomad FIN

AF:

0.231

Gnomad MID

AF:

0.278

Gnomad NFE

AF:

0.340

Gnomad OTH

AF:

0.301

GnomAD3 exomes

AF:

0.275

AC:

69042

AN:

251408

Hom.:

10714

AF XY:

0.284

AC XY:

38592

AN XY:

135888

show subpopulations

Gnomad AFR exome

AF:

0.238

Gnomad AMR exome

AF:

0.179

Gnomad ASJ exome

AF:

0.315

Gnomad EAS exome

AF:

0.0365

Gnomad SAS exome

AF:

0.315

Gnomad FIN exome

AF:

0.235

Gnomad NFE exome

AF:

0.339

Gnomad OTH exome

AF:

0.300

GnomAD4 exome

AF:

0.330

AC:

482471

AN:

1461288

Hom.:

83404

Cov.:

AF XY:

0.330

AC XY:

239891

AN XY:

726982

show subpopulations

Gnomad4 AFR exome

AF:

0.240

Gnomad4 AMR exome

AF:

0.183

Gnomad4 ASJ exome

AF:

0.313

Gnomad4 EAS exome

AF:

0.0400

Gnomad4 SAS exome

AF:

0.313

Gnomad4 FIN exome

AF:

0.240

Gnomad4 NFE exome

AF:

0.356

Gnomad4 OTH exome

AF:

0.324

GnomAD4 genome

AF:

0.282

AC:

42967

AN:

152128

Hom.:

6556

Cov.:

AF XY:

0.274

AC XY:

20372

AN XY:

74374

show subpopulations

Gnomad4 AFR

AF:

0.242

Gnomad4 AMR

AF:

0.236

Gnomad4 ASJ

AF:

0.315

Gnomad4 EAS

AF:

0.0445

Gnomad4 SAS

AF:

0.299

Gnomad4 FIN

AF:

0.231

Gnomad4 NFE

AF:

0.341

Gnomad4 OTH

AF:

0.298

Alfa

AF:

0.317

Hom.:

5547

Bravo

AF:

0.279

Asia WGS

AF:

0.190

AC:

662

AN:

3478

EpiCase

AF:

0.343

EpiControl

AF:

0.345

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.36

CADD

Benign

DANN

Benign

0.81

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

2.8

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