NM_198719.2:c.1078-15064A>G

Variant names:

• chr1-70989452-T-C
• rs2050066
• NM_198719.2:c.1078-15064A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 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 -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 rank	MANE	Protein	UniProt
PTGER3	NM_198719.2	c.1078-15064A>G		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.1078-15064A>G		intron_variant	Intron 2 of 3	1	NM_198719.2	ENSP00000302313.5

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

African (AFR) AF: 0.0408 AC: 1693 AN: 41530

American (AMR) AF: 0.0649 AC: 993 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.118 AC: 410 AN: 3470

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5186

South Asian (SAS) AF: 0.0273 AC: 132 AN: 4828

European-Finnish (FIN) AF: 0.0529 AC: 562 AN: 10614

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6877 AN: 68012

Other (OTH) AF: 0.0853 AC: 180 AN: 2110

Alfa AF: 0.0897 Hom.: 391

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
PhyloP100		-1.0
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: rs2050066; hg19: chr1-71455135;