rs164741

chr16-89625890-A-Gchr16-89625890-A-T

Variant summary

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

The NM_001389466.1(DPEP1):c.-106-4415A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.635 in 152,048 control chromosomes in the GnomAD database, including 31,813 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 0.64 (31813 hom., cov: 32)
• Consequence: DPEP1 NM_001389466.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

Genes affected

DPEP1 (HGNC:3002): (dipeptidase 1) The protein encoded by this gene is a kidney membrane enzyme involved in the metabolism of glutathione and other similar proteins by dipeptide hydrolysis. The encoded protein is known to regulate leukotriene activity by catalyzing the conversion of leukotriene D4 to leukotriene E4. This protein uses zinc as a cofactor and acts as a disulfide-linked homodimer. [provided by RefSeq, Dec 2020]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DPEP1	NM_001389466.1	c.-106-4415A>G		intron_variant		ENST00000690203.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DPEP1	ENST00000690203.1	c.-106-4415A>G		intron_variant			NM_001389466.1	P1

Frequencies

GnomAD3 genomes AF: 0.636 AC: 96566 AN: 151930 Hom.: 31799 Cov.: 32

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.760

Gnomad AMR AF: 0.566

Gnomad ASJ AF: 0.716

Gnomad EAS AF: 0.0929

Gnomad SAS AF: 0.674

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.635 AC: 96613 AN: 152048 Hom.: 31813 Cov.: 32 AF XY: 0.625 AC XY: 46488 AN XY: 74326

Gnomad4 AFR AF: 0.629

Gnomad4 AMR AF: 0.566

Gnomad4 ASJ AF: 0.716

Gnomad4 EAS AF: 0.0929

Gnomad4 SAS AF: 0.674

Gnomad4 FIN AF: 0.562

Gnomad4 NFE AF: 0.697

Gnomad4 OTH AF: 0.671

Alfa AF: 0.696 Hom.: 46877

Bravo AF: 0.627

Asia WGS AF: 0.377 AC: 1312 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.74
Dann	Benign	0.16

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: rs164741; hg19: chr16-89692298;