rs17848916

Variant names:

• chr2-162047874-A-C
• rs17848916
• NM_001935.4:c.95-373T>G

Your query was ambiguous. Multiple possible variants found:

• chr2-162047874-A-C
• chr2-162047874-A-G
• chr2-162047874-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001935.4(DPP4):​c.95-373T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.038 in 152,308 control chromosomes in the GnomAD database, including 249 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 0.038 (249 hom., cov: 32)
• Consequence: DPP4 NM_001935.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.374
• Publications: 2 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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 = 0.0949 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001935.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPP4	NM_001935.4	MANE Select	c.95-373T>G		intron	N/A	NP_001926.2
	DPP4	NM_001379604.1		c.95-376T>G		intron	N/A	NP_001366533.1	A0A7I2V2X8
	DPP4	NM_001379605.1		c.92-376T>G		intron	N/A	NP_001366534.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPP4	ENST00000360534.8	TSL:1 MANE Select	c.95-373T>G		intron	N/A	ENSP00000353731.3	P27487
	DPP4	ENST00000434918.6	TSL:1	n.95-376T>G		intron	N/A	ENSP00000402259.2	F8WE17
	DPP4	ENST00000461836.6	TSL:1	n.576-373T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0379 AC: 5770 AN: 152190 Hom.: 246 Cov.: 32

Gnomad AFR AF: 0.0974

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0246

Gnomad ASJ AF: 0.00576

Gnomad EAS AF: 0.0479

Gnomad SAS AF: 0.0246

Gnomad FIN AF: 0.00480

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0125

Gnomad OTH AF: 0.0307

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

GnomAD4 genome AF: 0.0380 AC: 5788 AN: 152308 Hom.: 249 Cov.: 32 AF XY: 0.0373 AC XY: 2781 AN XY: 74476

African (AFR) AF: 0.0974 AC: 4050 AN: 41560

American (AMR) AF: 0.0246 AC: 377 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.00576 AC: 20 AN: 3470

East Asian (EAS) AF: 0.0480 AC: 249 AN: 5188

South Asian (SAS) AF: 0.0246 AC: 119 AN: 4830

European-Finnish (FIN) AF: 0.00480 AC: 51 AN: 10620

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0125 AC: 851 AN: 68026

Other (OTH) AF: 0.0308 AC: 65 AN: 2110

Alfa AF: 0.0204 Hom.: 99

Bravo AF: 0.0418

Asia WGS AF: 0.0490 AC: 169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.2
DANN	Benign	0.75
PhyloP100		0.37
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17848916; hg19: chr2-162904384;