dbSNP rs1353411: PTGER2:c.-166G>A (chr14-52314383-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_000956.4(PTGER2):c.-166G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 779,840 control chromosomes in the GnomAD database, including 24,739 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 0.28 ( 6903 hom., cov: 32)

Exomes 𝑓: 0.21 ( 17836 hom. )

Consequence

PTGER2
NM_000956.4 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.35

Publications

14 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:

ENSG00000289424 (HGNC:):

ENSG00000289424 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.551 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTGER2	NM_000956.4 link	c.-166G>A		5_prime_UTR_variant	Exon 1 of 2	ENST00000245457.6	NP_000947.2	P43116

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
PTGER2	ENST00000245457.6 link	c.-166G>A	5_prime_UTR_variant	Exon 1 of 2	1	NM_000956.4	ENSP00000245457.5	P43116
PTGER2	ENST00000557436.2 link	c.-198G>A	5_prime_UTR_variant	Exon 1 of 3	3		ENSP00000450933.1	G3V2Y6
ENSG00000289424	ENST00000726802.1 link	n.356-631C>T	intron_variant	Intron 1 of 1
ENSG00000289424	ENST00000726803.1 link	n.-9C>T	upstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.277

AC:

42002

AN:

151750

Hom.:

6887

Cov.:

show subpopulations

Gnomad AFR

AF:

0.365

Gnomad AMI

AF:

0.214

Gnomad AMR

AF:

0.374

Gnomad ASJ

AF:

0.192

Gnomad EAS

AF:

0.568

Gnomad SAS

AF:

0.560

Gnomad FIN

AF:

0.165

Gnomad MID

AF:

0.264

Gnomad NFE

AF:

0.182

Gnomad OTH

AF:

0.266

GnomAD4 exome

AF:

0.214

AC:

134337

AN:

627982

Hom.:

17836

Cov.:

AF XY:

0.215

AC XY:

65330

AN XY:

304406

show subpopulations

African (AFR)

AF:

0.364

AC:

5103

AN:

14012

American (AMR)

AF:

0.395

AC:

3199

AN:

8102

Ashkenazi Jewish (ASJ)

AF:

0.189

AC:

2161

AN:

11404

East Asian (EAS)

AF:

0.577

AC:

13930

AN:

24152

South Asian (SAS)

AF:

0.561

AC:

5894

AN:

10504

European-Finnish (FIN)

AF:

0.184

AC:

4129

AN:

22472

Middle Eastern (MID)

AF:

0.284

AC:

588

AN:

2070

European-Non Finnish (NFE)

AF:

0.182

AC:

91968

AN:

506602

Other (OTH)

AF:

0.257

AC:

7365

AN:

28664

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.510

Heterozygous variant carriers

4732

9464

14195

18927

23659

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3336

6672

10008

13344

16680

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.277

AC:

42065

AN:

151858

Hom.:

6903

Cov.:

AF XY:

0.287

AC XY:

21337

AN XY:

74238

show subpopulations

African (AFR)

AF:

0.365

AC:

15126

AN:

41434

American (AMR)

AF:

0.374

AC:

5725

AN:

15290

Ashkenazi Jewish (ASJ)

AF:

0.192

AC:

666

AN:

3468

East Asian (EAS)

AF:

0.568

AC:

2895

AN:

5096

South Asian (SAS)

AF:

0.560

AC:

2692

AN:

4808

European-Finnish (FIN)

AF:

0.165

AC:

1746

AN:

10582

Middle Eastern (MID)

AF:

0.260

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.182

AC:

12379

AN:

67864

Other (OTH)

AF:

0.267

AC:

566

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1447

2895

4342

5790

7237

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

420

840

1260

1680

2100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.234

Hom.:

608

Bravo

AF:

0.292

Asia WGS

AF:

0.513

AC:

1785

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

(source)

DANN

Benign

0.94

PhyloP100

1.3

PromoterAI

-0.24

Neutral

(source)

Mutation Taster

=299/1

polymorphism (auto)

(source)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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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