Variant chr9-129748681-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_004878.5(PTGES):c.183C>T(p.Ser61=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00461 in 1,579,712 control chromosomes in the GnomAD database, including 263 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.024 ( 154 hom., cov: 32)

Exomes 𝑓: 0.0025 ( 109 hom. )

Consequence

PTGES
NM_004878.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -3.44

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 9-129748681-G-A is Benign according to our data. Variant chr9-129748681-G-A is described in ClinVar as [Benign]. Clinvar id is 768328.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-3.44 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0793 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTGES	NM_004878.5 linkuse as main transcript	c.183C>T	p.Ser61=	synonymous_variant	2/3	ENST00000340607.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTGES	ENST00000340607.5 linkuse as main transcript	c.183C>T	p.Ser61=	synonymous_variant	2/3	1	NM_004878.5	P1
PTGES	ENST00000481476.1 linkuse as main transcript	n.312C>T		non_coding_transcript_exon_variant	3/4	1

Frequencies

GnomAD3 genomes

AF:

0.0238

AC:

3627

AN:

152128

Hom.:

155

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0815

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0109

Gnomad ASJ

AF:

0.00115

Gnomad EAS

AF:

0.000964

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0127

Gnomad NFE

AF:

0.000573

Gnomad OTH

AF:

0.0163

GnomAD3 exomes

AF:

0.00643

AC:

1375

AN:

213678

Hom.:

AF XY:

0.00457

AC XY:

537

AN XY:

117538

show subpopulations

Gnomad AFR exome

AF:

0.0826

Gnomad AMR exome

AF:

0.00566

Gnomad ASJ exome

AF:

0.00146

Gnomad EAS exome

AF:

0.00206

Gnomad SAS exome

AF:

0.0000762

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000584

Gnomad OTH exome

AF:

0.00378

GnomAD4 exome

AF:

0.00255

AC:

3640

AN:

1427466

Hom.:

109

Cov.:

AF XY:

0.00226

AC XY:

1602

AN XY:

710206

show subpopulations

Gnomad4 AFR exome

AF:

0.0812

Gnomad4 AMR exome

AF:

0.00679

Gnomad4 ASJ exome

AF:

0.00116

Gnomad4 EAS exome

AF:

0.00228

Gnomad4 SAS exome

AF:

0.0000861

Gnomad4 FIN exome

AF:

0.0000188

Gnomad4 NFE exome

AF:

0.000360

Gnomad4 OTH exome

AF:

0.00585

GnomAD4 genome

AF:

0.0239

AC:

3641

AN:

152246

Hom.:

154

Cov.:

AF XY:

0.0231

AC XY:

1720

AN XY:

74448

show subpopulations

Gnomad4 AFR

AF:

0.0816

Gnomad4 AMR

AF:

0.0108

Gnomad4 ASJ

AF:

0.00115

Gnomad4 EAS

AF:

0.000966

Gnomad4 SAS

AF:

0.000414

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000573

Gnomad4 OTH

AF:

0.0161

Alfa

AF:

0.0128

Hom.:

Bravo

AF:

0.0275

Asia WGS

AF:

0.00664

AC:

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Oct 10, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

0.22

DANN

Benign

0.60

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over