rs5673

Variant names:

• chr1-71012158-A-T
• rs5673
• ENST00000370924: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

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTGER3	NM_198719.2	c.1077+147T>A		intron_variant	Intron 2 of 3	ENST00000306666.10	NP_942012.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTGER3	ENST00000306666.10	c.1077+147T>A		intron_variant	Intron 2 of 3	1	NM_198719.2	ENSP00000302313.5

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

Gnomad4 AFR exome AF: 0.148 AC: 4686 AN: 31636

Gnomad4 AMR exome AF: 0.0565 AC: 2111 AN: 37348

Gnomad4 ASJ exome AF: 0.108 AC: 2426 AN: 22508

Gnomad4 EAS exome AF: 0.000357 AC: 14 AN: 39168

Gnomad4 SAS exome AF: 0.0271 AC: 2053 AN: 75798

Gnomad4 FIN exome AF: 0.0443 AC: 1810 AN: 40818

Gnomad4 NFE exome AF: 0.0806 AC: 87426 AN: 1085294

Gnomad4 Remaining exome 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

Gnomad4 AFR AF: 0.146 AC: 0.145767 AN: 0.145767

Gnomad4 AMR AF: 0.0685 AC: 0.0685146 AN: 0.0685146

Gnomad4 ASJ AF: 0.111 AC: 0.110502 AN: 0.110502

Gnomad4 EAS AF: 0.000386 AC: 0.000385951 AN: 0.000385951

Gnomad4 SAS AF: 0.0215 AC: 0.0215321 AN: 0.0215321

Gnomad4 FIN AF: 0.0440 AC: 0.0439985 AN: 0.0439985

Gnomad4 NFE AF: 0.0823 AC: 0.0822969 AN: 0.0822969

Gnomad4 OTH AF: 0.0994 AC: 0.0994318 AN: 0.0994318

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	18
DANN	Benign	0.86
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

Publications

LitVar

Other links and lift over

dbSNP: rs5673; hg19: chr1-71477841;