Variant 5-40681152-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_000958.3(PTGER4):c.159C>T(p.Thr53Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0713 in 1,614,044 control chromosomes in the GnomAD database, including 4,537 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 0.083 ( 578 hom., cov: 32)

Exomes 𝑓: 0.070 ( 3959 hom. )

Consequence

PTGER4
NM_000958.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.604

Variant links:

Genes affected

PTGER4 (HGNC:9596): (prostaglandin E receptor 4) The protein encoded by this gene is a member of the G-protein coupled receptor family. This protein is one of four receptors identified for prostaglandin E2 (PGE2). This receptor can activate T-cell factor signaling. It has been shown to mediate PGE2 induced expression of early growth response 1 (EGR1), regulate the level and stability of cyclooxygenase-2 mRNA, and lead to the phosphorylation of glycogen synthase kinase-3. Knockout studies in mice suggest that this receptor may be involved in the neonatal adaptation of circulatory system, osteoporosis, as well as initiation of skin immune responses. [provided by RefSeq, Jul 2008]

PTGER4 links:

PTGER4 (HGNC:):

PTGER4 links:

TTC33 (HGNC:29959): (tetratricopeptide repeat domain 33)

TTC33 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.51).

BP7

Synonymous conserved (PhyloP=0.604 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.108 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTGER4	NM_000958.3 linkuse as main transcript	c.159C>T	p.Thr53Thr	synonymous_variant	2/3	ENST00000302472.4	NP_000949.1	P35408A0PJF5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTGER4	ENST00000302472.4 linkuse as main transcript	c.159C>T	p.Thr53Thr	synonymous_variant	2/3	1	NM_000958.3	ENSP00000302846.3		P35408

Frequencies

GnomAD3 genomes

AF:

0.0829

AC:

12608

AN:

152058

Hom.:

577

Cov.:

show subpopulations

Gnomad AFR

AF:

0.111

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.0563

Gnomad ASJ

AF:

0.0787

Gnomad EAS

AF:

0.00116

Gnomad SAS

AF:

0.0367

Gnomad FIN

AF:

0.136

Gnomad MID

AF:

0.0823

Gnomad NFE

AF:

0.0749

Gnomad OTH

AF:

0.0651

GnomAD3 exomes

AF:

0.0653

AC:

16408

AN:

251398

Hom.:

717

AF XY:

0.0646

AC XY:

8781

AN XY:

135906

show subpopulations

Gnomad AFR exome

AF:

0.107

Gnomad AMR exome

AF:

0.0360

Gnomad ASJ exome

AF:

0.0699

Gnomad EAS exome

AF:

0.000653

Gnomad SAS exome

AF:

0.0403

Gnomad FIN exome

AF:

0.125

Gnomad NFE exome

AF:

0.0734

Gnomad OTH exome

AF:

0.0693

GnomAD4 exome

AF:

0.0701

AC:

102531

AN:

1461868

Hom.:

3959

Cov.:

AF XY:

0.0696

AC XY:

50633

AN XY:

727232

show subpopulations

Gnomad4 AFR exome

AF:

0.107

Gnomad4 AMR exome

AF:

0.0370

Gnomad4 ASJ exome

AF:

0.0765

Gnomad4 EAS exome

AF:

0.000630

Gnomad4 SAS exome

AF:

0.0419

Gnomad4 FIN exome

AF:

0.123

Gnomad4 NFE exome

AF:

0.0724

Gnomad4 OTH exome

AF:

0.0688

GnomAD4 genome

AF:

0.0829

AC:

12621

AN:

152176

Hom.:

578

Cov.:

AF XY:

0.0837

AC XY:

6231

AN XY:

74408

show subpopulations

Gnomad4 AFR

AF:

0.111

Gnomad4 AMR

AF:

0.0562

Gnomad4 ASJ

AF:

0.0787

Gnomad4 EAS

AF:

0.00135

Gnomad4 SAS

AF:

0.0367

Gnomad4 FIN

AF:

0.136

Gnomad4 NFE

AF:

0.0749

Gnomad4 OTH

AF:

0.0644

Alfa

AF:

0.0737

Hom.:

576

Bravo

AF:

0.0770

Asia WGS

AF:

0.0270

AC:

AN:

3478

EpiCase

AF:

0.0709

EpiControl

AF:

0.0650

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.51

CADD

Benign

DANN

Benign

0.95

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over