1-71014966-G-A

Variant names:

• chr1-71014966-G-A
• rs2206344
• NM_198719.2:c.898-2482C>T

Variant summary

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

The NM_198719.2(PTGER3):​c.898-2482C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.919 in 152,298 control chromosomes in the GnomAD database, including 64,418 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 0.92 (64418 hom., cov: 32)
• Consequence: PTGER3 NM_198719.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.40
• Publications: 6 publications found

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.966 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTGER3	NM_198719.2	c.898-2482C>T		intron_variant	Intron 1 of 3	ENST00000306666.10	NP_942012.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTGER3	ENST00000306666.10	c.898-2482C>T		intron_variant	Intron 1 of 3	1	NM_198719.2	ENSP00000302313.5

Frequencies

GnomAD3 genomes AF: 0.919 AC: 139800 AN: 152180 Hom.: 64351 Cov.: 32

Gnomad AFR AF: 0.974

Gnomad AMI AF: 0.971

Gnomad AMR AF: 0.923

Gnomad ASJ AF: 0.910

Gnomad EAS AF: 0.958

Gnomad SAS AF: 0.869

Gnomad FIN AF: 0.893

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.888

Gnomad OTH AF: 0.920

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

GnomAD4 genome AF: 0.919 AC: 139928 AN: 152298 Hom.: 64418 Cov.: 32 AF XY: 0.919 AC XY: 68426 AN XY: 74460

African (AFR) AF: 0.974 AC: 40484 AN: 41568

American (AMR) AF: 0.923 AC: 14124 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.910 AC: 3158 AN: 3472

East Asian (EAS) AF: 0.958 AC: 4959 AN: 5176

South Asian (SAS) AF: 0.870 AC: 4199 AN: 4828

European-Finnish (FIN) AF: 0.893 AC: 9470 AN: 10602

Middle Eastern (MID) AF: 0.952 AC: 280 AN: 294

European-Non Finnish (NFE) AF: 0.888 AC: 60422 AN: 68038

Other (OTH) AF: 0.921 AC: 1946 AN: 2114

Alfa AF: 0.903 Hom.: 93514

Bravo AF: 0.926

Asia WGS AF: 0.930 AC: 3235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.37
DANN	Benign	0.50
PhyloP100		-2.4
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs2206344; hg19: chr1-71480649;