chr2-162044379-C-T

Position:

• chr2-162044379-C-T

Variant summary

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

The NM_001935.4(DPP4):​c.366+1153G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.146 in 151,674 control chromosomes in the GnomAD database, including 2,117 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 0.15 (2117 hom., cov: 31)
• Consequence: DPP4 NM_001935.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.899

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DPP4	NM_001935.4	c.366+1153G>A		intron_variant		ENST00000360534.8	NP_001926.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DPP4	ENST00000360534.8	c.366+1153G>A		intron_variant		1	NM_001935.4	ENSP00000353731.3

Frequencies

GnomAD3 genomes AF: 0.146 AC: 22064 AN: 151556 Hom.: 2120 Cov.: 31

Gnomad AFR AF: 0.0893

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.146 AC: 22072 AN: 151674 Hom.: 2117 Cov.: 31 AF XY: 0.149 AC XY: 11069 AN XY: 74074

Gnomad4 AFR AF: 0.0894

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.514

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.203

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.124

Alfa AF: 0.127 Hom.: 1078

Bravo AF: 0.145

Asia WGS AF: 0.283 AC: 981 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	20
DANN	Benign	0.79
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs3788979; hg19: chr2-162900889;