rs884115

chr9-128125577-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_025072.7(PTGES2):c.280-136G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 805,602 control chromosomes in the GnomAD database, including 17,448 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 0.26 (7539 hom., cov: 32)
  • Exomes 𝑓: 0.15 (9909 hom.)
• Consequence: PTGES2 NM_025072.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.82

Genes affected

PTGES2 (HGNC:17822): (prostaglandin E synthase 2) The protein encoded by this gene is a membrane-associated prostaglandin E synthase, which catalyzes the conversion of prostaglandin H2 to prostaglandin E2. This protein also has been shown to activate the transcription regulated by a gamma-interferon-activated transcription element (GATE). Multiple transcript variants have been found for this gene. [provided by RefSeq, Jun 2009]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTGES2	NM_025072.7	c.280-136G>A		intron_variant		ENST00000338961.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTGES2	ENST00000338961.11	c.280-136G>A		intron_variant		1	NM_025072.7	P2

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38684 AN: 151826 Hom.: 7499 Cov.: 32

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.192

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.232

Gnomad FIN AF: 0.0929

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.246

GnomAD4 exome AF: 0.149 AC: 97603 AN: 653658 Hom.: 9909 AF XY: 0.151 AC XY: 51050 AN XY: 338402

Gnomad4 AFR exome AF: 0.555

Gnomad4 AMR exome AF: 0.230

Gnomad4 ASJ exome AF: 0.190

Gnomad4 EAS exome AF: 0.235

Gnomad4 SAS exome AF: 0.227

Gnomad4 FIN exome AF: 0.0939

Gnomad4 NFE exome AF: 0.114

Gnomad4 OTH exome AF: 0.168

GnomAD4 genome AF: 0.255 AC: 38779 AN: 151944 Hom.: 7539 Cov.: 32 AF XY: 0.254 AC XY: 18872 AN XY: 74266

Gnomad4 AFR AF: 0.550

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.192

Gnomad4 EAS AF: 0.179

Gnomad4 SAS AF: 0.231

Gnomad4 FIN AF: 0.0929

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.249

Alfa AF: 0.157 Hom.: 1486

Bravo AF: 0.276

Asia WGS AF: 0.255 AC: 884 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.29
Dann	Benign	0.28

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

LitVar

Other links and lift over

dbSNP: rs884115; hg19: chr9-130887856;