19-14476048-C-T

Variant names:

• chr19-14476048-C-T
• rs3810255
• ENST00000883541.1:c.-18+1204G>A

Variant summary

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

The ENST00000883541.1(PTGER1):​c.-18+1204G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.138 in 151,986 control chromosomes in the GnomAD database, including 2,214 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 0.14 (2214 hom., cov: 31)
• Consequence: PTGER1 ENST00000883541.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.512
• Publications: 6 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.597 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000883541.1. 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	ENST00000883541.1		c.-18+1204G>A		intron	N/A	ENSP00000553600.1
	PTGER1	ENST00000883542.1		c.-18+73G>A		intron	N/A	ENSP00000553601.1
	PTGER1	ENST00000947755.1		c.-18+823G>A		intron	N/A	ENSP00000617814.1

Frequencies

GnomAD3 genomes AF: 0.138 AC: 20973 AN: 151868 Hom.: 2208 Cov.: 31

Gnomad AFR AF: 0.0643

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.170

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.138 AC: 20990 AN: 151986 Hom.: 2214 Cov.: 31 AF XY: 0.142 AC XY: 10553 AN XY: 74288

African (AFR) AF: 0.0641 AC: 2659 AN: 41460

American (AMR) AF: 0.170 AC: 2606 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 453 AN: 3470

East Asian (EAS) AF: 0.615 AC: 3156 AN: 5132

South Asian (SAS) AF: 0.206 AC: 991 AN: 4820

European-Finnish (FIN) AF: 0.114 AC: 1213 AN: 10598

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.139 AC: 9416 AN: 67902

Other (OTH) AF: 0.142 AC: 299 AN: 2112

Alfa AF: 0.132 Hom.: 2368

Bravo AF: 0.142

Asia WGS AF: 0.387 AC: 1348 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	12
DANN	Benign	0.75
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs3810255; hg19: chr19-14586860;