rs255049

Positions:

• chr16-67979568-T-C

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.261

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
DPEP3	NM_001370198.1	c.414+71A>G		intron_variant		ENST00000268793.6	NP_001357127.1
DPEP3	NM_001129758.2	c.414+71A>G		intron_variant			NP_001123230.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
DPEP3	ENST00000268793.6	c.414+71A>G		intron_variant		1	NM_001370198.1	ENSP00000268793.5
DPEP3	ENST00000672962.1	c.489+71A>G		intron_variant				ENSP00000500237.1
DPEP3	ENST00000574342.1	n.415+526A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50634 AN: 151984 Hom.: 11848 Cov.: 32

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

Gnomad4 AFR exome AF: 0.693

Gnomad4 AMR exome AF: 0.224

Gnomad4 ASJ exome AF: 0.238

Gnomad4 EAS exome AF: 0.137

Gnomad4 SAS exome AF: 0.264

Gnomad4 FIN exome AF: 0.216

Gnomad4 NFE exome AF: 0.190

Gnomad4 OTH exome AF: 0.226

GnomAD4 genome AF: 0.333 AC: 50722 AN: 152102 Hom.: 11878 Cov.: 32 AF XY: 0.331 AC XY: 24627 AN XY: 74336

Gnomad4 AFR AF: 0.671

Gnomad4 AMR AF: 0.252

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.221

Gnomad4 NFE AF: 0.192

Gnomad4 OTH AF: 0.308

Alfa AF: 0.220 Hom.: 7244

Bravo AF: 0.347

Asia WGS AF: 0.262 AC: 912 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	5.9
DANN	Benign	0.74

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: rs255049; hg19: chr16-68013471; COSMIC: COSV52050274;