16-67979690-G-A

Variant names:

• chr16-67979690-G-A
• rs56921747
• NM_001370198.1:c.363C>T

Variant summary

Our verdict is Benign. The variant received -15 ACMG points: 0P and 15B. BP4_Strong BP6_Moderate BP7 BS1 BS2

The NM_001370198.1(DPEP3):​c.363C>T​(p.Ser121Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00116 in 1,614,120 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0063 (11 hom., cov: 32)
  • Exomes 𝑓: 0.00063 (13 hom.)
• Consequence: DPEP3 NM_001370198.1 synonymous
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.221

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]

ACMG classification

Our verdict: Benign. The variant received -15 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 16-67979690-G-A is Benign according to our data. Variant chr16-67979690-G-A is described in ClinVar as [Benign]. Clinvar id is 731125.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-0.221 with no splicing effect.
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0063 (960/152308) while in subpopulation AFR AF = 0.022 (916/41560). AF 95% confidence interval is 0.0209. There are 11 homozygotes in GnomAd4. There are 472 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 11 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DPEP3	NM_001370198.1	c.363C>T	p.Ser121Ser	synonymous_variant	Exon 2 of 10	ENST00000268793.6	NP_001357127.1
DPEP3	NM_001129758.2	c.363C>T	p.Ser121Ser	synonymous_variant	Exon 2 of 10		NP_001123230.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DPEP3	ENST00000268793.6	c.363C>T	p.Ser121Ser	synonymous_variant	Exon 2 of 10	1	NM_001370198.1	ENSP00000268793.5
DPEP3	ENST00000672962.1	c.438C>T	p.Ser146Ser	synonymous_variant	Exon 2 of 10			ENSP00000500237.1
DPEP3	ENST00000574342.1	n.415+404C>T		intron_variant	Intron 1 of 1	3

Frequencies

GnomAD3 genomes AF: 0.00631 AC: 961 AN: 152190 Hom.: 11 Cov.: 32

Gnomad AFR AF: 0.0221

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00209

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000588

Gnomad OTH AF: 0.00383

GnomAD2 exomes AF: 0.00169 AC: 425 AN: 251300 AF XY: 0.00130

Gnomad AFR exome AF: 0.0239

Gnomad AMR exome AF: 0.000897

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.000652

GnomAD4 exome AF: 0.000628 AC: 918 AN: 1461812 Hom.: 13 Cov.: 32 AF XY: 0.000551 AC XY: 401 AN XY: 727210

African (AFR) AF: 0.0241 AC: 806 AN: 33478

American (AMR) AF: 0.000984 AC: 44 AN: 44718

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26134

East Asian (EAS) AF: 0.00 AC: 0 AN: 39698

South Asian (SAS) AF: 0.0000116 AC: 1 AN: 86256

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53400

Middle Eastern (MID) AF: 0.000174 AC: 1 AN: 5758

European-Non Finnish (NFE) AF: 0.00000630 AC: 7 AN: 1111982

Other (OTH) AF: 0.000977 AC: 59 AN: 60388

GnomAD4 genome AF: 0.00630 AC: 960 AN: 152308 Hom.: 11 Cov.: 32 AF XY: 0.00634 AC XY: 472 AN XY: 74482

African (AFR) AF: 0.0220 AC: 916 AN: 41560

American (AMR) AF: 0.00209 AC: 32 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3468

East Asian (EAS) AF: 0.00 AC: 0 AN: 5178

South Asian (SAS) AF: 0.00 AC: 0 AN: 4830

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10624

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000588 AC: 4 AN: 68026

Other (OTH) AF: 0.00379 AC: 8 AN: 2112

Alfa AF: 0.00328 Hom.: 2

Bravo AF: 0.00694

Asia WGS AF: 0.000866 AC: 3 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Nov 15, 2018

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.1
DANN	Benign	0.52
PhyloP100		-0.22
Mutation Taster		=100/0	polymorphism

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

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Other links and lift over

dbSNP: rs56921747; hg19: chr16-68013593;