rs2744918

chr1-71018884-G-Achr1-71018884-G-Cchr1-71018884-G-T

Variant summary

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

The NM_198719.2(PTGER3):c.898-6400C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.914 in 152,194 control chromosomes in the GnomAD database, including 63,627 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 0.91 (63627 hom., cov: 31)
• Consequence: PTGER3 NM_198719.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.33

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=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTGER3	NM_198719.2	c.898-6400C>T		intron_variant		ENST00000306666.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTGER3	ENST00000306666.10	c.898-6400C>T		intron_variant		1	NM_198719.2	A1

Frequencies

GnomAD3 genomes AF: 0.914 AC: 138948 AN: 152076 Hom.: 63565 Cov.: 31

Gnomad AFR AF: 0.957

Gnomad AMI AF: 0.971

Gnomad AMR AF: 0.920

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.958

Gnomad SAS AF: 0.869

Gnomad FIN AF: 0.894

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.888

Gnomad OTH AF: 0.915

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

GnomAD4 genome AF: 0.914 AC: 139071 AN: 152194 Hom.: 63627 Cov.: 31 AF XY: 0.914 AC XY: 67991 AN XY: 74392

Gnomad4 AFR AF: 0.957

Gnomad4 AMR AF: 0.920

Gnomad4 ASJ AF: 0.910

Gnomad4 EAS AF: 0.958

Gnomad4 SAS AF: 0.870

Gnomad4 FIN AF: 0.894

Gnomad4 NFE AF: 0.888

Gnomad4 OTH AF: 0.916

Alfa AF: 0.896 Hom.: 24173

Bravo AF: 0.920

Asia WGS AF: 0.928 AC: 3229 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	13
Dann	Benign	0.38

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: rs2744918; hg19: chr1-71484567;