rs11209716

chr1-70911967-T-C

Variant summary

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

The ENST00000370931.7(PTGER3):c.*23+41796A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 151,772 control chromosomes in the GnomAD database, including 10,195 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 0.36 (10195 hom., cov: 31)
• Consequence: PTGER3 ENST00000370931.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTGER3	NM_198714.2	c.*23+41796A>G		intron_variant
PTGER3	NM_198716.2	c.1104+41796A>G		intron_variant
PTGER3	NM_198717.2	c.1078-59108A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTGER3	ENST00000370931.7	c.*23+41796A>G		intron_variant		1		A1
PTGER3	ENST00000460330.5	c.1104+41796A>G		intron_variant		1		A2
PTGER3	ENST00000628037.2	c.1078-59108A>G		intron_variant		1		P4

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55155 AN: 151654 Hom.: 10194 Cov.: 31

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.387

Gnomad ASJ AF: 0.514

Gnomad EAS AF: 0.299

Gnomad SAS AF: 0.270

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.364 AC: 55175 AN: 151772 Hom.: 10195 Cov.: 31 AF XY: 0.357 AC XY: 26452 AN XY: 74140

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.514

Gnomad4 EAS AF: 0.299

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.384

Gnomad4 OTH AF: 0.392

Alfa AF: 0.390 Hom.: 16218

Bravo AF: 0.378

Asia WGS AF: 0.276 AC: 961 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.58
Dann	Benign	0.60

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11209716; hg19: chr1-71377650;