dbSNP rs255049: DPEP3:c.414+71A>G (chr16-67979568-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001370198.1(DPEP3):c.414+71A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 1,592,654 control chromosomes in the GnomAD database, including 48,301 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 0.33 ( 11878 hom., cov: 32)

Exomes 𝑓: 0.21 ( 36423 hom. )

Consequence

DPEP3
NM_001370198.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.261

Publications

78 publications found

Variant links:

Genes affected

DPEP3 (HGNC:23029): (dipeptidase 3) This gene encodes a membrane-bound glycoprotein from the family of dipeptidases involved in hydrolytic metabolism of various dipeptides, including penem and carbapenem beta-lactam antibiotics. This gene is located on chromosome 16 in a cluster with another member of this family. Alternatively spliced transcript variants that encode different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

DPEP3 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.664 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001370198.1. 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
	DPEP3	NM_001370198.1	MANE Select	c.414+71A>G		intron	N/A	NP_001357127.1	Q9H4B8
	DPEP3	NM_001129758.2		c.414+71A>G		intron	N/A	NP_001123230.2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
DPEP3	ENST00000268793.6	TSL:1 MANE Select	c.414+71A>G	intron	N/A	ENSP00000268793.5	Q9H4B8
DPEP3	ENST00000672962.1		c.489+71A>G	intron	N/A	ENSP00000500237.1	A0A5F9ZHB4
DPEP3	ENST00000876631.1		c.414+71A>G	intron	N/A	ENSP00000546690.1

Frequencies

GnomAD3 genomes

AF:

0.333

AC:

50634

AN:

151984

Hom.:

11848

Cov.:

show subpopulations

Gnomad AFR

AF:

0.670

Gnomad AMI

AF:

0.274

Gnomad AMR

AF:

0.252

Gnomad ASJ

AF:

0.234

Gnomad EAS

AF:

0.116

Gnomad SAS

AF:

0.255

Gnomad FIN

AF:

0.221

Gnomad MID

AF:

0.354

Gnomad NFE

AF:

0.192

Gnomad OTH

AF:

0.306

GnomAD4 exome

AF:

0.209

AC:

300490

AN:

1440552

Hom.:

36423

AF XY:

0.209

AC XY:

149300

AN XY:

714796

show subpopulations

African (AFR)

AF:

0.693

AC:

22945

AN:

33120

American (AMR)

AF:

0.224

AC:

9732

AN:

43466

Ashkenazi Jewish (ASJ)

AF:

0.238

AC:

5948

AN:

25002

East Asian (EAS)

AF:

0.137

AC:

5376

AN:

39384

South Asian (SAS)

AF:

0.264

AC:

22112

AN:

83834

European-Finnish (FIN)

AF:

0.216

AC:

11032

AN:

51190

Middle Eastern (MID)

AF:

0.263

AC:

1104

AN:

4200

European-Non Finnish (NFE)

AF:

0.190

AC:

208801

AN:

1101004

Other (OTH)

AF:

0.226

AC:

13440

AN:

59352

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

11878

23756

35634

47512

59390

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

7538

15076

22614

30152

37690

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.333

AC:

50722

AN:

152102

Hom.:

11878

Cov.:

AF XY:

0.331

AC XY:

24627

AN XY:

74336

show subpopulations

African (AFR)

AF:

0.671

AC:

27808

AN:

41468

American (AMR)

AF:

0.252

AC:

3845

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.234

AC:

810

AN:

3468

East Asian (EAS)

AF:

0.116

AC:

602

AN:

5168

South Asian (SAS)

AF:

0.255

AC:

1227

AN:

4816

European-Finnish (FIN)

AF:

0.221

AC:

2344

AN:

10590

Middle Eastern (MID)

AF:

0.347

AC:

102

AN:

294

European-Non Finnish (NFE)

AF:

0.192

AC:

13082

AN:

67996

Other (OTH)

AF:

0.308

AC:

652

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1417

2834

4252

5669

7086

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

442

884

1326

1768

2210

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.238

Hom.:

19936

Bravo

AF:

0.347

Asia WGS

AF:

0.262

AC:

912

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

5.9

(source)

DANN

Benign

0.74

PhyloP100

0.26

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over