chr1-71019616-T-C

Position:

• chr1-71019616-T-C

Variant summary

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

The NM_198719.2(PTGER3):​c.898-7132A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.331 in 152,150 control chromosomes in the GnomAD database, including 9,056 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 0.33 (9056 hom., cov: 32)
• Consequence: PTGER3 NM_198719.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00900

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=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.438 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PTGER3	NM_198719.2	c.898-7132A>G		intron_variant		ENST00000306666.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PTGER3	ENST00000306666.10	c.898-7132A>G		intron_variant		1	NM_198719.2	A1

Frequencies

GnomAD3 genomes AF: 0.331 AC: 50392 AN: 152030 Hom.: 9060 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.399

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.331 AC: 50380 AN: 152150 Hom.: 9056 Cov.: 32 AF XY: 0.334 AC XY: 24860 AN XY: 74366

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.329

Gnomad4 EAS AF: 0.288

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.407

Gnomad4 NFE AF: 0.399

Gnomad4 OTH AF: 0.335

Alfa AF: 0.385 Hom.: 5761

Bravo AF: 0.316

Asia WGS AF: 0.382 AC: 1331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.2
DANN	Benign	0.65

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: rs2268062; hg19: chr1-71485299;