rs2050066

Positions:

• chr1-70989452-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.1078-15064A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0723 in 152,256 control chromosomes in the GnomAD database, including 532 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 0.072 (532 hom., cov: 32)
• Consequence: PTGER3 NM_198719.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0991 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTGER3	NM_198719.2	c.1078-15064A>G		intron_variant		ENST00000306666.10	NP_942012.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTGER3	ENST00000306666.10	c.1078-15064A>G		intron_variant		1	NM_198719.2	ENSP00000302313	A1

Frequencies

GnomAD3 genomes AF: 0.0723 AC: 10994 AN: 152138 Hom.: 530 Cov.: 32

Gnomad AFR AF: 0.0405

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.0650

Gnomad ASJ AF: 0.118

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0271

Gnomad FIN AF: 0.0529

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0862

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

GnomAD4 genome AF: 0.0723 AC: 11007 AN: 152256 Hom.: 532 Cov.: 32 AF XY: 0.0684 AC XY: 5095 AN XY: 74454

Gnomad4 AFR AF: 0.0408

Gnomad4 AMR AF: 0.0649

Gnomad4 ASJ AF: 0.118

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0273

Gnomad4 FIN AF: 0.0529

Gnomad4 NFE AF: 0.101

Gnomad4 OTH AF: 0.0853

Alfa AF: 0.0894 Hom.: 351

Bravo AF: 0.0726

Asia WGS AF: 0.0200 AC: 68 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.68

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: rs2050066; hg19: chr1-71455135;