rs594454

chr1-70964785-G-T

Variant summary

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

The ENST00000356595.8(PTGER3):c.1078-10996C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.604 in 151,966 control chromosomes in the GnomAD database, including 28,277 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 0.60 (28277 hom., cov: 32)
• Consequence: PTGER3 ENST00000356595.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.175

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.701 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTGER3	NM_001126044.2	c.1169+9512C>A		intron_variant
PTGER3	NM_198714.2	c.1169+9512C>A		intron_variant
PTGER3	NM_198716.2	c.1078-10996C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTGER3	ENST00000356595.8	c.1078-10996C>A		intron_variant		1
PTGER3	ENST00000370931.7	c.1169+9512C>A		intron_variant		1		A1
PTGER3	ENST00000460330.5	c.1078-10996C>A		intron_variant		1		A2

Frequencies

GnomAD3 genomes AF: 0.604 AC: 91782 AN: 151846 Hom.: 28246 Cov.: 32

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.577

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.625

Gnomad OTH AF: 0.644

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.604 AC: 91862 AN: 151966 Hom.: 28277 Cov.: 32 AF XY: 0.609 AC XY: 45265 AN XY: 74272

Gnomad4 AFR AF: 0.508

Gnomad4 AMR AF: 0.704

Gnomad4 ASJ AF: 0.631

Gnomad4 EAS AF: 0.720

Gnomad4 SAS AF: 0.679

Gnomad4 FIN AF: 0.605

Gnomad4 NFE AF: 0.625

Gnomad4 OTH AF: 0.644

Alfa AF: 0.620 Hom.: 5981

Bravo AF: 0.610

Asia WGS AF: 0.708 AC: 2464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	4.1
Dann	Benign	0.24

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: rs594454; hg19: chr1-71430468; COSMIC: COSV63036295;