Genetic Variant PTGER2:c.-166G>C (chr14-52314383-G-C) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_000956.4(PTGER2):c.-166G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

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:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.71).

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

628976

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

304910

African (AFR)

AF:

0.00

AC:

AN:

14048

American (AMR)

AF:

0.00

AC:

AN:

8118

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

11410

East Asian (EAS)

AF:

0.00

AC:

AN:

24178

South Asian (SAS)

AF:

0.00

AC:

AN:

10536

European-Finnish (FIN)

AF:

0.00

AC:

AN:

22494

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2070

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

507414

Other (OTH)

AF:

0.00

AC:

AN:

28708

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

(source)

DANN

Benign

0.78

PhyloP100

1.3

PromoterAI

-0.0038

Neutral

(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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over