rs5673

Variant names:

• chr1-71012158-A-T
• rs5673
• ENST00000370924.5:c.*57T>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_198715.3(PTGER3):​c.*57T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0774 in 1,547,932 control chromosomes in the GnomAD database, including 5,207 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 0.092 (791 hom., cov: 33)
  • Exomes 𝑓: 0.076 (4416 hom.)
• Consequence: PTGER3 NM_198715.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.20
• Publications: 13 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198715.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTGER3	NM_198719.2	MANE Select	c.1077+147T>A		intron	N/A	NP_942012.1	P43115-1
	PTGER3	NM_198715.3		c.*57T>A		3_prime_UTR	Exon 2 of 2	NP_942008.1	P43115-2
	PTGER3	NM_198718.2		c.1077+147T>A		intron	N/A	NP_942011.1	P43115-5

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTGER3	ENST00000370924.5	TSL:1	c.*57T>A		3_prime_UTR	Exon 2 of 2	ENSP00000359962.3	P43115-2
	PTGER3	ENST00000306666.10	TSL:1 MANE Select	c.1077+147T>A		intron	N/A	ENSP00000302313.5	P43115-1
	PTGER3	ENST00000356595.8	TSL:1	c.1077+147T>A		intron	N/A	ENSP00000349003.4	P43115-5

Frequencies

GnomAD3 genomes AF: 0.0915 AC: 13926 AN: 152142 Hom.: 788 Cov.: 33

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.0687

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0213

Gnomad FIN AF: 0.0440

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0823

Gnomad OTH AF: 0.100

GnomAD4 exome AF: 0.0758 AC: 105806 AN: 1395672 Hom.: 4416 Cov.: 33 AF XY: 0.0744 AC XY: 51197 AN XY: 688452

African (AFR) AF: 0.148 AC: 4686 AN: 31636

American (AMR) AF: 0.0565 AC: 2111 AN: 37348

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 2426 AN: 22508

East Asian (EAS) AF: 0.000357 AC: 14 AN: 39168

South Asian (SAS) AF: 0.0271 AC: 2053 AN: 75798

European-Finnish (FIN) AF: 0.0443 AC: 1810 AN: 40818

Middle Eastern (MID) AF: 0.144 AC: 746 AN: 5198

European-Non Finnish (NFE) AF: 0.0806 AC: 87426 AN: 1085294

Other (OTH) AF: 0.0783 AC: 4534 AN: 57904

GnomAD4 genome AF: 0.0917 AC: 13955 AN: 152260 Hom.: 791 Cov.: 33 AF XY: 0.0878 AC XY: 6535 AN XY: 74456

African (AFR) AF: 0.146 AC: 6054 AN: 41532

American (AMR) AF: 0.0685 AC: 1048 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 383 AN: 3466

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5182

South Asian (SAS) AF: 0.0215 AC: 104 AN: 4830

European-Finnish (FIN) AF: 0.0440 AC: 467 AN: 10614

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.0823 AC: 5598 AN: 68022

Other (OTH) AF: 0.0994 AC: 210 AN: 2112

Alfa AF: 0.0846 Hom.: 87

Bravo AF: 0.0969

Asia WGS AF: 0.0230 AC: 80 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	18
DANN	Benign	0.86
PhyloP100		2.2
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: rs5673; hg19: chr1-71477841;