rs594454

Variant names:

• chr1-70964785-G-T
• rs594454
• ENST00000356595.8:c.1078-10996C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000356595.8. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTGER3	NM_198718.2		c.1078-10996C>A		intron	N/A	NP_942011.1
	PTGER3	NM_001126044.2		c.1169+9512C>A		intron	N/A	NP_001119516.1
	PTGER3	NM_198714.2		c.1169+9512C>A		intron	N/A	NP_942007.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTGER3	ENST00000356595.8	TSL:1	c.1078-10996C>A		intron	N/A	ENSP00000349003.4
	PTGER3	ENST00000370931.7	TSL:1	c.1169+9512C>A		intron	N/A	ENSP00000359969.3
	PTGER3	ENST00000460330.5	TSL:1	c.1078-10996C>A		intron	N/A	ENSP00000418073.1

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

African (AFR) AF: 0.508 AC: 21002 AN: 41382

American (AMR) AF: 0.704 AC: 10759 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.631 AC: 2191 AN: 3470

East Asian (EAS) AF: 0.720 AC: 3724 AN: 5172

South Asian (SAS) AF: 0.679 AC: 3276 AN: 4824

European-Finnish (FIN) AF: 0.605 AC: 6400 AN: 10570

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.625 AC: 42457 AN: 67954

Other (OTH) AF: 0.644 AC: 1357 AN: 2108

Alfa AF: 0.623 Hom.: 11073

Bravo AF: 0.610

Asia WGS AF: 0.708 AC: 2464 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	4.1
DANN	Benign	0.24
PhyloP100		0.17
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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