rs3765894

chr1-71015115-A-G

Variant summary

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

The NM_198719.2(PTGER3):c.898-2631T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 151,820 control chromosomes in the GnomAD database, including 9,041 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 0.33 (9041 hom., cov: 32)
• Consequence: PTGER3 NM_198719.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.657

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=-1.04).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTGER3	NM_198719.2	c.898-2631T>C		intron_variant		ENST00000306666.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTGER3	ENST00000306666.10	c.898-2631T>C		intron_variant		1	NM_198719.2	A1

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50352 AN: 151702 Hom.: 9045 Cov.: 32

Gnomad AFR AF: 0.188

Gnomad AMI AF: 0.385

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.332 AC: 50339 AN: 151820 Hom.: 9041 Cov.: 32 AF XY: 0.335 AC XY: 24827 AN XY: 74152

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.330

Gnomad4 EAS AF: 0.288

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.399

Gnomad4 OTH AF: 0.337

Alfa AF: 0.384 Hom.: 5759

Bravo AF: 0.316

Asia WGS AF: 0.382 AC: 1331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.88
Dann	Benign	0.50

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: rs3765894; hg19: chr1-71480798;