ENST00000883542.1:c.-154T>G

Variant names:

• chr19-14476257-A-C
• rs3810253
• ENST00000883542.1:c.-154T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000883542.1(PTGER1):​c.-154T>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 151,204 control chromosomes in the GnomAD database, including 11,611 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 0.34 (11611 hom., cov: 29)
• Consequence: PTGER1 ENST00000883542.1 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.439
• Publications: 7 publications found

Genes affected

PTGER1 (HGNC:9593): (prostaglandin E receptor 1) 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). Through a phosphatidylinositol-calcium second messenger system, G-Q proteins mediate this receptor's activity. Knockout studies in mice suggested a role of this receptor in mediating algesia and in regulation of blood pressure. Studies in mice also suggested that this gene may mediate adrenocorticotropic hormone response to bacterial endotoxin. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000883542.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTGER1	ENST00000883542.1		c.-154T>G		5_prime_UTR	Exon 1 of 3	ENSP00000553601.1
	PTGER1	ENST00000883541.1		c.-18+995T>G		intron	N/A	ENSP00000553600.1
	PTGER1	ENST00000947755.1		c.-18+614T>G		intron	N/A	ENSP00000617814.1

Frequencies

GnomAD3 genomes AF: 0.344 AC: 52036 AN: 151086 Hom.: 11565 Cov.: 29

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.353

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.728

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.345 AC: 52138 AN: 151204 Hom.: 11611 Cov.: 29 AF XY: 0.348 AC XY: 25668 AN XY: 73812

African (AFR) AF: 0.585 AC: 24095 AN: 41208

American (AMR) AF: 0.354 AC: 5381 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.230 AC: 799 AN: 3468

East Asian (EAS) AF: 0.727 AC: 3697 AN: 5082

South Asian (SAS) AF: 0.346 AC: 1644 AN: 4758

European-Finnish (FIN) AF: 0.202 AC: 2116 AN: 10456

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13415 AN: 67732

Other (OTH) AF: 0.326 AC: 684 AN: 2098

Alfa AF: 0.253 Hom.: 14147

Bravo AF: 0.369

Asia WGS AF: 0.557 AC: 1938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.4
DANN	Benign	0.62
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs3810253; hg19: chr19-14587069;