dbSNP rs2302821: PTGES:n.597T>G (chr9-129739602-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000481476.1(PTGES):n.597T>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 0.12 in 1,548,682 control chromosomes in the GnomAD database, including 20,091 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 ( 4119 hom., cov: 32)

Exomes 𝑓: 0.11 ( 15972 hom. )

Consequence

PTGES
ENST00000481476.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.70

Publications

18 publications found

Variant links:

Genes affected

PTGES (HGNC:9599): (prostaglandin E synthase) The protein encoded by this gene is a glutathione-dependent prostaglandin E synthase. The expression of this gene has been shown to be induced by proinflammatory cytokine interleukin 1 beta (IL1B). Its expression can also be induced by tumor suppressor protein TP53, and may be involved in TP53 induced apoptosis. Knockout studies in mice suggest that this gene may contribute to the pathogenesis of collagen-induced arthritis and mediate acute pain during inflammatory responses. [provided by RefSeq, Jul 2008]

PTGES 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=-0.9).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.536 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTGES	NM_004878.5 link	c.*9T>G		3_prime_UTR_variant	Exon 3 of 3	ENST00000340607.5	NP_004869.1	O14684

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTGES	ENST00000481476.1 link	n.597T>G		non_coding_transcript_exon_variant	Exon 4 of 4	1
PTGES	ENST00000340607.5 link	c.*9T>G		3_prime_UTR_variant	Exon 3 of 3	1	NM_004878.5	ENSP00000342385.4		O14684

Frequencies

GnomAD3 genomes

AF:

0.187

AC:

28369

AN:

152042

Hom.:

4110

Cov.:

show subpopulations

Gnomad AFR

AF:

0.361

Gnomad AMI

AF:

0.0439

Gnomad AMR

AF:

0.149

Gnomad ASJ

AF:

0.0476

Gnomad EAS

AF:

0.553

Gnomad SAS

AF:

0.283

Gnomad FIN

AF:

0.0882

Gnomad MID

AF:

0.101

Gnomad NFE

AF:

0.0802

Gnomad OTH

AF:

0.144

GnomAD2 exomes

AF:

0.171

AC:

26438

AN:

154458

AF XY:

0.171

show subpopulations

Gnomad AFR exome

AF:

0.369

Gnomad AMR exome

AF:

0.176

Gnomad ASJ exome

AF:

0.0451

Gnomad EAS exome

AF:

0.552

Gnomad FIN exome

AF:

0.0942

Gnomad NFE exome

AF:

0.0774

Gnomad OTH exome

AF:

0.119

GnomAD4 exome

AF:

0.112

AC:

157055

AN:

1396522

Hom.:

15972

Cov.:

AF XY:

0.115

AC XY:

79199

AN XY:

688608

show subpopulations

African (AFR)

AF:

0.373

AC:

11774

AN:

31552

American (AMR)

AF:

0.172

AC:

6133

AN:

35644

Ashkenazi Jewish (ASJ)

AF:

0.0429

AC:

1076

AN:

25070

East Asian (EAS)

AF:

0.574

AC:

20474

AN:

35700

South Asian (SAS)

AF:

0.249

AC:

19665

AN:

79130

European-Finnish (FIN)

AF:

0.0955

AC:

4601

AN:

48196

Middle Eastern (MID)

AF:

0.0834

AC:

446

AN:

5348

European-Non Finnish (NFE)

AF:

0.0792

AC:

85348

AN:

1077982

Other (OTH)

AF:

0.130

AC:

7538

AN:

57900

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.490

Heterozygous variant carriers

7156

14311

21467

28622

35778

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3544

7088

10632

14176

17720

<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:

0.187

AC:

28413

AN:

152160

Hom.:

4119

Cov.:

AF XY:

0.191

AC XY:

14216

AN XY:

74390

show subpopulations

African (AFR)

AF:

0.361

AC:

14998

AN:

41508

American (AMR)

AF:

0.149

AC:

2280

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.0476

AC:

165

AN:

3470

East Asian (EAS)

AF:

0.553

AC:

2839

AN:

5134

South Asian (SAS)

AF:

0.283

AC:

1364

AN:

4822

European-Finnish (FIN)

AF:

0.0882

AC:

935

AN:

10606

Middle Eastern (MID)

AF:

0.105

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0802

AC:

5455

AN:

68006

Other (OTH)

AF:

0.145

AC:

306

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

1048

2095

3143

4190

5238

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

298

596

894

1192

1490

<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:

0.118

Hom.:

5800

Bravo

AF:

0.199

Asia WGS

AF:

0.370

AC:

1287

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.092

(source)

DANN

Benign

0.49

PhyloP100

-1.7

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