rs2300167

chr1-70992479-T-C

Variant summary

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

The NM_198719.2(PTGER3):c.1078-18091A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 152,134 control chromosomes in the GnomAD database, including 8,577 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 0.32 (8577 hom., cov: 33)
• Consequence: PTGER3 NM_198719.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.277

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.425 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTGER3	NM_198719.2	c.1078-18091A>G		intron_variant		ENST00000306666.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTGER3	ENST00000306666.10	c.1078-18091A>G		intron_variant		1	NM_198719.2	A1

Frequencies

GnomAD3 genomes AF: 0.324 AC: 49216 AN: 152016 Hom.: 8581 Cov.: 33

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.344

Gnomad ASJ AF: 0.336

Gnomad EAS AF: 0.285

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.323 AC: 49208 AN: 152134 Hom.: 8577 Cov.: 33 AF XY: 0.327 AC XY: 24318 AN XY: 74364

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.343

Gnomad4 ASJ AF: 0.336

Gnomad4 EAS AF: 0.285

Gnomad4 SAS AF: 0.440

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.382

Gnomad4 OTH AF: 0.330

Alfa AF: 0.375 Hom.: 14539

Bravo AF: 0.310

Asia WGS AF: 0.377 AC: 1313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.4
Dann	Benign	0.60

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: rs2300167; hg19: chr1-71458162;