rs17541777

chr1-70909817-T-Cchr1-70909817-T-G

Variant summary

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

The ENST00000370931.7(PTGER3):c.*23+43946A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.115 in 152,294 control chromosomes in the GnomAD database, including 1,321 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 0.11 (1321 hom., cov: 32)
• Consequence: PTGER3 ENST00000370931.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTGER3	NM_198714.2	c.*23+43946A>G		intron_variant
PTGER3	NM_198716.2	c.1104+43946A>G		intron_variant
PTGER3	NM_198717.2	c.1078-56958A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTGER3	ENST00000370931.7	c.*23+43946A>G		intron_variant		1		A1
PTGER3	ENST00000460330.5	c.1104+43946A>G		intron_variant		1		A2
PTGER3	ENST00000628037.2	c.1078-56958A>G		intron_variant		1		P4

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17505 AN: 152176 Hom.: 1323 Cov.: 32

Gnomad AFR AF: 0.0449

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0498

Gnomad FIN AF: 0.0997

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.115 AC: 17499 AN: 152294 Hom.: 1321 Cov.: 32 AF XY: 0.111 AC XY: 8257 AN XY: 74468

Gnomad4 AFR AF: 0.0448

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.240

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.0501

Gnomad4 FIN AF: 0.0997

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.154

Alfa AF: 0.156 Hom.: 1833

Bravo AF: 0.117

Asia WGS AF: 0.0340 AC: 118 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	5.3
Dann	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17541777; hg19: chr1-71375500;