Genetic Variant PTGER3:c.*57T>A (chr1-71012158-A-T) – ACMG Classification: Benign (-10 pts)

Variant summary

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

The ENST00000370924.5(PTGER3):c.*57T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0774 in 1,547,932 control chromosomes in the GnomAD database, including 5,207 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 0.092 ( 791 hom., cov: 33)

Exomes 𝑓: 0.076 ( 4416 hom. )

Consequence

PTGER3
ENST00000370924.5 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.20

Publications

13 publications found

Variant links:

Genes affected

PTGER3 (HGNC:9595): (prostaglandin E receptor 3) 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 may have many biological functions, which involve digestion, nervous system, kidney reabsorption, and uterine contraction activities. Studies of the mouse counterpart suggest that this receptor may also mediate adrenocorticotropic hormone response as well as fever generation in response to exogenous and endogenous stimuli. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2009]

PTGER3 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=-0.44).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTGER3	NM_198719.2 link	c.1077+147T>A		intron_variant	Intron 2 of 3	ENST00000306666.10	NP_942012.1	P43115-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTGER3	ENST00000306666.10 link	c.1077+147T>A		intron_variant	Intron 2 of 3	1	NM_198719.2	ENSP00000302313.5		P43115-1

Frequencies

GnomAD3 genomes

AF:

0.0915

AC:

13926

AN:

152142

Hom.:

788

Cov.:

show subpopulations

Gnomad AFR

AF:

0.145

Gnomad AMI

AF:

0.0603

Gnomad AMR

AF:

0.0687

Gnomad ASJ

AF:

0.111

Gnomad EAS

AF:

0.000385

Gnomad SAS

AF:

0.0213

Gnomad FIN

AF:

0.0440

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.0823

Gnomad OTH

AF:

0.100

GnomAD4 exome

AF:

0.0758

AC:

105806

AN:

1395672

Hom.:

4416

Cov.:

AF XY:

0.0744

AC XY:

51197

AN XY:

688452

show subpopulations

African (AFR)

AF:

0.148

AC:

4686

AN:

31636

American (AMR)

AF:

0.0565

AC:

2111

AN:

37348

Ashkenazi Jewish (ASJ)

AF:

0.108

AC:

2426

AN:

22508

East Asian (EAS)

AF:

0.000357

AC:

AN:

39168

South Asian (SAS)

AF:

0.0271

AC:

2053

AN:

75798

European-Finnish (FIN)

AF:

0.0443

AC:

1810

AN:

40818

Middle Eastern (MID)

AF:

0.144

AC:

746

AN:

5198

European-Non Finnish (NFE)

AF:

0.0806

AC:

87426

AN:

1085294

Other (OTH)

AF:

0.0783

AC:

4534

AN:

57904

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

5535

11071

16606

22142

27677

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3266

6532

9798

13064

16330

<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:

0.0917

AC:

13955

AN:

152260

Hom.:

791

Cov.:

AF XY:

0.0878

AC XY:

6535

AN XY:

74456

show subpopulations

African (AFR)

AF:

0.146

AC:

6054

AN:

41532

American (AMR)

AF:

0.0685

AC:

1048

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.111

AC:

383

AN:

3466

East Asian (EAS)

AF:

0.000386

AC:

AN:

5182

South Asian (SAS)

AF:

0.0215

AC:

104

AN:

4830

European-Finnish (FIN)

AF:

0.0440

AC:

467

AN:

10614

Middle Eastern (MID)

AF:

0.116

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0823

AC:

5598

AN:

68022

Other (OTH)

AF:

0.0994

AC:

210

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

641

1282

1923

2564

3205

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

146

292

438

584

730

<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:

0.0846

Hom.:

Bravo

AF:

0.0969

Asia WGS

AF:

0.0230

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.44

CADD

Benign

(source)

DANN

Benign

0.86

PhyloP100

2.2

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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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