Genetic Variant PTGER2:c.*62T>C (chr14-52327516-T-C) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_000956.4(PTGER2):c.*62T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.827 in 1,328,124 control chromosomes in the GnomAD database, including 461,405 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 0.78 ( 46838 hom., cov: 32)

Exomes 𝑓: 0.83 ( 414567 hom. )

Consequence

PTGER2
NM_000956.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.45

Publications

17 publications found

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 Gene-Disease associations (from GenCC):

asthma, nasal polyps, and aspirin intolerance
Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics

PTGER2 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.37).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTGER2	NM_000956.4 link	c.*62T>C		3_prime_UTR_variant	Exon 2 of 2	ENST00000245457.6	NP_000947.2	P43116

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTGER2	ENST00000245457.6 link	c.*62T>C		3_prime_UTR_variant	Exon 2 of 2	1	NM_000956.4	ENSP00000245457.5		P43116
PTGER2	ENST00000557436.2 link	c.*62T>C		3_prime_UTR_variant	Exon 3 of 3	3		ENSP00000450933.1		G3V2Y6

Frequencies

GnomAD3 genomes

AF:

0.776

AC:

118025

AN:

152016

Hom.:

46816

Cov.:

show subpopulations

Gnomad AFR

AF:

0.652

Gnomad AMI

AF:

0.876

Gnomad AMR

AF:

0.774

Gnomad ASJ

AF:

0.857

Gnomad EAS

AF:

0.589

Gnomad SAS

AF:

0.531

Gnomad FIN

AF:

0.802

Gnomad MID

AF:

0.807

Gnomad NFE

AF:

0.874

Gnomad OTH

AF:

0.794

GnomAD4 exome

AF:

0.833

AC:

980022

AN:

1175990

Hom.:

414567

Cov.:

AF XY:

0.825

AC XY:

488373

AN XY:

591774

show subpopulations

African (AFR)

AF:

0.644

AC:

16980

AN:

26348

American (AMR)

AF:

0.777

AC:

25232

AN:

32470

Ashkenazi Jewish (ASJ)

AF:

0.858

AC:

18550

AN:

21626

East Asian (EAS)

AF:

0.593

AC:

22527

AN:

37998

South Asian (SAS)

AF:

0.549

AC:

39657

AN:

72222

European-Finnish (FIN)

AF:

0.795

AC:

34306

AN:

43162

Middle Eastern (MID)

AF:

0.806

AC:

4100

AN:

5084

European-Non Finnish (NFE)

AF:

0.877

AC:

777617

AN:

886510

Other (OTH)

AF:

0.812

AC:

41053

AN:

50570

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

7463

14927

22390

29854

37317

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.776

AC:

118093

AN:

152134

Hom.:

46838

Cov.:

AF XY:

0.767

AC XY:

57040

AN XY:

74376

show subpopulations

African (AFR)

AF:

0.652

AC:

27037

AN:

41476

American (AMR)

AF:

0.774

AC:

11840

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.857

AC:

2975

AN:

3472

East Asian (EAS)

AF:

0.589

AC:

3053

AN:

5180

South Asian (SAS)

AF:

0.532

AC:

2561

AN:

4810

European-Finnish (FIN)

AF:

0.802

AC:

8480

AN:

10576

Middle Eastern (MID)

AF:

0.806

AC:

237

AN:

294

European-Non Finnish (NFE)

AF:

0.874

AC:

59439

AN:

68010

Other (OTH)

AF:

0.792

AC:

1672

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1264

2528

3792

5056

6320

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.845

Hom.:

71427

Bravo

AF:

0.772

Asia WGS

AF:

0.618

AC:

2147

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.37

CADD

Benign

(source)

DANN

Benign

0.91

PhyloP100

1.5

Mutation Taster

=100/0

polymorphism (auto)

(source)

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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14-52327516-T-C

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over