Variant chr2-162008558-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001935.4(DPP4):c.1987+4T>C variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00267 in 1,612,816 control chromosomes in the GnomAD database, including 94 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0026 ( 4 hom., cov: 32)

Exomes 𝑓: 0.0027 ( 90 hom. )

Consequence

DPP4
NM_001935.4 splice_donor_region, intron

Scores

Splicing: ADA: 0.00007068

Clinical Significance

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

Conservation

PhyloP100: -0.570

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.75).

BP6

Variant 2-162008558-A-G is Benign according to our data. Variant chr2-162008558-A-G is described in ClinVar as [Benign]. Clinvar id is 715707.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAdExome4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0543 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.1987+4T>C		splice_donor_region_variant, intron_variant		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.1987+4T>C		splice_donor_region_variant, intron_variant		1	NM_001935.4	ENSP00000353731	P3

Frequencies

GnomAD3 genomes

AF:

0.00263

AC:

399

AN:

151984

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000750

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00958

Gnomad ASJ

AF:

0.00115

Gnomad EAS

AF:

0.0291

Gnomad SAS

AF:

0.00290

Gnomad FIN

AF:

0.000189

Gnomad MID

AF:

0.00633

Gnomad NFE

AF:

0.000647

Gnomad OTH

AF:

0.00239

GnomAD3 exomes

AF:

0.00521

AC:

1306

AN:

250884

Hom.:

AF XY:

0.00425

AC XY:

576

AN XY:

135580

show subpopulations

Gnomad AFR exome

AF:

0.00111

Gnomad AMR exome

AF:

0.0183

Gnomad ASJ exome

AF:

0.00129

Gnomad EAS exome

AF:

0.0256

Gnomad SAS exome

AF:

0.00206

Gnomad FIN exome

AF:

0.000324

Gnomad NFE exome

AF:

0.000697

Gnomad OTH exome

AF:

0.00392

GnomAD4 exome

AF:

0.00267

AC:

3907

AN:

1460714

Hom.:

Cov.:

AF XY:

0.00259

AC XY:

1880

AN XY:

726724

show subpopulations

Gnomad4 AFR exome

AF:

0.000239

Gnomad4 AMR exome

AF:

0.0172

Gnomad4 ASJ exome

AF:

0.000881

Gnomad4 EAS exome

AF:

0.0563

Gnomad4 SAS exome

AF:

0.00241

Gnomad4 FIN exome

AF:

0.000206

Gnomad4 NFE exome

AF:

0.000469

Gnomad4 OTH exome

AF:

0.00219

GnomAD4 genome

AF:

0.00263

AC:

400

AN:

152102

Hom.:

Cov.:

AF XY:

0.00288

AC XY:

214

AN XY:

74346

show subpopulations

Gnomad4 AFR

AF:

0.000747

Gnomad4 AMR

AF:

0.00963

Gnomad4 ASJ

AF:

0.00115

Gnomad4 EAS

AF:

0.0292

Gnomad4 SAS

AF:

0.00291

Gnomad4 FIN

AF:

0.000189

Gnomad4 NFE

AF:

0.000647

Gnomad4 OTH

AF:

0.00237

Alfa

AF:

0.00206

Hom.:

Bravo

AF:

0.00393

Asia WGS

AF:

0.0180

AC:

AN:

3478

EpiCase

AF:

0.000437

EpiControl

AF:

0.000356

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

-0.75

CADD

Benign

6.8

DANN

Benign

0.83

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000071

dbscSNV1_RF

Benign

0.082

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over