chr1-70962159-C-A

Position:

• chr1-70962159-C-A

Variant summary

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

The NM_198718.2(PTGER3):​c.1078-8370G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 152,166 control chromosomes in the GnomAD database, including 1,969 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 0.13 (1969 hom., cov: 33)
• Consequence: PTGER3 NM_198718.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.973

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]

PTGER3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PTGER3	NM_198718.2	c.1078-8370G>T		intron_variant			NP_942011.1
PTGER3	NM_001126044.2	c.1170-8370G>T		intron_variant			NP_001119516.1
PTGER3	NM_198714.2	c.1170-8370G>T		intron_variant			NP_942007.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PTGER3	ENST00000356595.8	c.1078-8370G>T		intron_variant		1		ENSP00000349003.4
PTGER3	ENST00000370931.7	c.1170-8370G>T		intron_variant		1		ENSP00000359969.3
PTGER3	ENST00000460330.5	c.1078-8370G>T		intron_variant		1		ENSP00000418073.1

Frequencies

GnomAD3 genomes AF: 0.129 AC: 19647 AN: 152048 Hom.: 1959 Cov.: 33

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.0757

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0243

Gnomad FIN AF: 0.0504

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0889

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.129 AC: 19689 AN: 152166 Hom.: 1969 Cov.: 33 AF XY: 0.125 AC XY: 9326 AN XY: 74406

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.0755

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.000964

Gnomad4 SAS AF: 0.0245

Gnomad4 FIN AF: 0.0504

Gnomad4 NFE AF: 0.0889

Gnomad4 OTH AF: 0.128

Alfa AF: 0.0938 Hom.: 971

Bravo AF: 0.138

Asia WGS AF: 0.0300 AC: 103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.65
DANN	Benign	0.75

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: rs6665776; hg19: chr1-71427842;