Variant chr2-162008614-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBA1

The NM_001935.4(DPP4):c.1935C>T(p.Gly645=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00403 in 1,613,384 control chromosomes in the GnomAD database, including 128 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0053 ( 20 hom., cov: 32)

Exomes 𝑓: 0.0039 ( 108 hom. )

Consequence

DPP4
NM_001935.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.850

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP6

Variant 2-162008614-G-A is Benign according to our data. Variant chr2-162008614-G-A is described in ClinVar as [Benign]. Clinvar id is 708761.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0511 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DPP4	NM_001935.4 linkuse as main transcript	c.1935C>T	p.Gly645=	synonymous_variant	22/26	ENST00000360534.8	NP_001926.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DPP4	ENST00000360534.8 linkuse as main transcript	c.1935C>T	p.Gly645=	synonymous_variant	22/26	1	NM_001935.4	ENSP00000353731	P3

Frequencies

GnomAD3 genomes

AF:

0.00529

AC:

803

AN:

151800

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000726

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00335

Gnomad ASJ

AF:

0.000576

Gnomad EAS

AF:

0.0336

Gnomad SAS

AF:

0.00376

Gnomad FIN

AF:

0.0453

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00107

Gnomad OTH

AF:

0.00240

GnomAD3 exomes

AF:

0.00828

AC:

2080

AN:

251270

Hom.:

AF XY:

0.00793

AC XY:

1077

AN XY:

135814

show subpopulations

Gnomad AFR exome

AF:

0.0000616

Gnomad AMR exome

AF:

0.00431

Gnomad ASJ exome

AF:

0.00109

Gnomad EAS exome

AF:

0.0366

Gnomad SAS exome

AF:

0.00216

Gnomad FIN exome

AF:

0.0422

Gnomad NFE exome

AF:

0.00205

Gnomad OTH exome

AF:

0.00554

GnomAD4 exome

AF:

0.00390

AC:

5693

AN:

1461466

Hom.:

108

Cov.:

AF XY:

0.00390

AC XY:

2833

AN XY:

727074

show subpopulations

Gnomad4 AFR exome

AF:

0.000149

Gnomad4 AMR exome

AF:

0.00401

Gnomad4 ASJ exome

AF:

0.00111

Gnomad4 EAS exome

AF:

0.0530

Gnomad4 SAS exome

AF:

0.00269

Gnomad4 FIN exome

AF:

0.0374

Gnomad4 NFE exome

AF:

0.000839

Gnomad4 OTH exome

AF:

0.00348

GnomAD4 genome

AF:

0.00529

AC:

803

AN:

151918

Hom.:

Cov.:

AF XY:

0.00760

AC XY:

564

AN XY:

74222

show subpopulations

Gnomad4 AFR

AF:

0.0000724

Gnomad4 AMR

AF:

0.00334

Gnomad4 ASJ

AF:

0.000576

Gnomad4 EAS

AF:

0.0339

Gnomad4 SAS

AF:

0.00377

Gnomad4 FIN

AF:

0.0453

Gnomad4 NFE

AF:

0.00107

Gnomad4 OTH

AF:

0.00190

Alfa

AF:

0.00113

Hom.:

Bravo

AF:

0.00301

Asia WGS

AF:

0.0230

AC:

AN:

3478

EpiCase

AF:

0.000655

EpiControl

AF:

0.000889

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 31, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.55

CADD

Benign

0.80

DANN

Benign

0.53

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.24

Details are displayed if max score is > 0.2

DS_AL_spliceai

0.24

Position offset: 47

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over