Genetic Variant PTGER3:n.*346A>G (chr1-70852578-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000361210.6(PTGER3):n.*346A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 509,536 control chromosomes in the GnomAD database, including 14,234 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 0.19 ( 3505 hom., cov: 32)

Exomes 𝑓: 0.23 ( 10729 hom. )

Consequence

PTGER3
ENST00000361210.6 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0100

Publications

22 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:

ENSG00000235782 (HGNC:40481):

ENSG00000235782 links:

LOC102724572 (HGNC:):

LOC102724572 links:

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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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.375 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
PTGER3	NR_028292.2 link	n.1794A>G	non_coding_transcript_exon_variant	Exon 6 of 6
PTGER3	NR_028293.2 link	n.1767A>G	non_coding_transcript_exon_variant	Exon 5 of 5
PTGER3	NR_028294.2 link	n.1863A>G	non_coding_transcript_exon_variant	Exon 6 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein	UniProt
PTGER3	ENST00000361210.6 link	n.*346A>G	non_coding_transcript_exon_variant	Exon 6 of 6	1	ENSP00000424340.1	O00325
PTGER3	ENST00000479353.5 link	n.*346A>G	non_coding_transcript_exon_variant	Exon 5 of 5	1	ENSP00000421583.1	P43115-7
PTGER3	ENST00000497146.5 link	n.*346A>G	non_coding_transcript_exon_variant	Exon 6 of 6	1	ENSP00000423561.1	A0A0B4J204

Frequencies

GnomAD3 genomes

AF:

0.191

AC:

29059

AN:

152040

Hom.:

3495

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0771

Gnomad AMI

AF:

0.242

Gnomad AMR

AF:

0.338

Gnomad ASJ

AF:

0.187

Gnomad EAS

AF:

0.389

Gnomad SAS

AF:

0.319

Gnomad FIN

AF:

0.116

Gnomad MID

AF:

0.196

Gnomad NFE

AF:

0.215

Gnomad OTH

AF:

0.191

GnomAD4 exome

AF:

0.231

AC:

82417

AN:

357378

Hom.:

10729

Cov.:

AF XY:

0.236

AC XY:

44394

AN XY:

188082

show subpopulations

African (AFR)

AF:

0.0760

AC:

657

AN:

8642

American (AMR)

AF:

0.378

AC:

3974

AN:

10506

Ashkenazi Jewish (ASJ)

AF:

0.193

AC:

2205

AN:

11452

East Asian (EAS)

AF:

0.384

AC:

9206

AN:

23972

South Asian (SAS)

AF:

0.310

AC:

9410

AN:

30318

European-Finnish (FIN)

AF:

0.133

AC:

3549

AN:

26628

Middle Eastern (MID)

AF:

0.180

AC:

302

AN:

1674

European-Non Finnish (NFE)

AF:

0.217

AC:

48363

AN:

222976

Other (OTH)

AF:

0.224

AC:

4751

AN:

21210

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

2853

5706

8558

11411

14264

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

274

548

822

1096

1370

<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:

0.191

AC:

29078

AN:

152158

Hom.:

3505

Cov.:

AF XY:

0.193

AC XY:

14363

AN XY:

74384

show subpopulations

African (AFR)

AF:

0.0770

AC:

3200

AN:

41532

American (AMR)

AF:

0.338

AC:

5167

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.187

AC:

648

AN:

3472

East Asian (EAS)

AF:

0.390

AC:

2015

AN:

5172

South Asian (SAS)

AF:

0.318

AC:

1536

AN:

4828

European-Finnish (FIN)

AF:

0.116

AC:

1226

AN:

10580

Middle Eastern (MID)

AF:

0.194

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.215

AC:

14598

AN:

67982

Other (OTH)

AF:

0.195

AC:

411

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1159

2318

3477

4636

5795

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

322

644

966

1288

1610

<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:

0.210

Hom.:

6488

Bravo

AF:

0.203

Asia WGS

AF:

0.333

AC:

1156

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.4

(source)

DANN

Benign

0.79

PhyloP100

-0.010

Mutation Taster

=100/0

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