Variant chr14-52314795-T-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 1P and 16B. PP3BP4_StrongBP6_Very_StrongBS2

The NM_000956.4(PTGER2):c.247T>G(p.Cys83Gly) variant causes a missense change. The variant allele was found at a frequency of 0.00578 in 1,612,730 control chromosomes in the GnomAD database, including 38 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0052 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0058 ( 36 hom. )

Consequence

PTGER2
NM_000956.4 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 6.25

Variant links:

Genes affected

PTGER2 (HGNC:9594): (prostaglandin E receptor 2) This gene encodes a receptor for prostaglandin E2, a metabolite of arachidonic acid which has different biologic activities in a wide range of tissues. Mutations in this gene are associated with aspirin-induced susceptibility to asthma. [provided by RefSeq, Oct 2009]

PTGER2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

PP3

Multiple lines of computational evidence support a deleterious effect 6: BayesDel_noAF, Cadd, Eigen, FATHMM_MKL, MutationAssessor, PROVEAN [when BayesDel_addAF, max_spliceai, MetaRNN, MutationTaster was below the threshold]

BP4

Computational evidence support a benign effect (MetaRNN=0.016982645).

BP6

Variant 14-52314795-T-G is Benign according to our data. Variant chr14-52314795-T-G is described in ClinVar as [Likely_benign]. Clinvar id is 710814.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTGER2	NM_000956.4 linkuse as main transcript	c.247T>G	p.Cys83Gly	missense_variant	1/2	ENST00000245457.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTGER2	ENST00000245457.6 linkuse as main transcript	c.247T>G	p.Cys83Gly	missense_variant	1/2	1	NM_000956.4	P1
PTGER2	ENST00000557436.1 linkuse as main transcript	c.-80+294T>G		intron_variant		3

Frequencies

GnomAD3 genomes

AF:

0.00521

AC:

793

AN:

152178

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00140

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00733

Gnomad ASJ

AF:

0.0121

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000622

Gnomad FIN

AF:

0.00151

Gnomad MID

AF:

0.0190

Gnomad NFE

AF:

0.00785

Gnomad OTH

AF:

0.0105

GnomAD3 exomes

AF:

0.00550

AC:

1361

AN:

247292

Hom.:

AF XY:

0.00554

AC XY:

746

AN XY:

134546

show subpopulations

Gnomad AFR exome

AF:

0.000966

Gnomad AMR exome

AF:

0.00643

Gnomad ASJ exome

AF:

0.0122

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00108

Gnomad FIN exome

AF:

0.00125

Gnomad NFE exome

AF:

0.00819

Gnomad OTH exome

AF:

0.00561

GnomAD4 exome

AF:

0.00584

AC:

8527

AN:

1460434

Hom.:

Cov.:

AF XY:

0.00580

AC XY:

4217

AN XY:

726448

show subpopulations

Gnomad4 AFR exome

AF:

0.00105

Gnomad4 AMR exome

AF:

0.00673

Gnomad4 ASJ exome

AF:

0.0118

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00116

Gnomad4 FIN exome

AF:

0.00124

Gnomad4 NFE exome

AF:

0.00656

Gnomad4 OTH exome

AF:

0.00639

GnomAD4 genome

AF:

0.00520

AC:

792

AN:

152296

Hom.:

Cov.:

AF XY:

0.00530

AC XY:

395

AN XY:

74468

show subpopulations

Gnomad4 AFR

AF:

0.00139

Gnomad4 AMR

AF:

0.00732

Gnomad4 ASJ

AF:

0.0121

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000415

Gnomad4 FIN

AF:

0.00151

Gnomad4 NFE

AF:

0.00785

Gnomad4 OTH

AF:

0.0104

Alfa

AF:

0.00640

Hom.:

Bravo

AF:

0.00532

TwinsUK

AF:

0.00297

AC:

ALSPAC

AF:

0.00415

AC:

ESP6500AA

AF:

0.000688

AC:

ESP6500EA

AF:

0.00872

AC:

ExAC

AF:

0.00530

AC:

641

Asia WGS

AF:

0.00173

AC:

AN:

3478

EpiCase

AF:

0.0114

EpiControl

AF:

0.00984

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Aug 01, 2023	PTGER2: BS2 -
Benign, criteria provided, single submitter	clinical testing	Invitae	Jun 28, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.39

BayesDel_addAF

Benign

-0.066

BayesDel_noAF

Pathogenic

0.14

CADD

Pathogenic

DANN

Uncertain

0.98

DEOGEN2

Uncertain

0.59

Eigen

Pathogenic

0.70

Eigen_PC

Uncertain

0.63

FATHMM_MKL

Uncertain

0.97

LIST_S2

Uncertain

0.86

MetaRNN

Benign

0.017

MetaSVM

Benign

-0.62

MutationAssessor

Pathogenic

3.1

MutationTaster

Benign

1.0

D;D

PrimateAI

Uncertain

0.76

PROVEAN

Pathogenic

-10

REVEL

Uncertain

0.55

Sift

Uncertain

0.014

Sift4G

Uncertain

0.017

Polyphen

1.0

Vest4

0.61

MVP

0.68

MPC

2.0

ClinPred

0.058

GERP RS

4.9

Varity_R

0.95

gMVP

0.69

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over