1-70929000-T-C

Variant names:

• chr1-70929000-T-C
• rs578096
• ENST00000370931.7:c.*23+24763A>G

Variant summary

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

The NM_198714.2(PTGER3):​c.*23+24763A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.896 in 152,134 control chromosomes in the GnomAD database, including 61,271 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 0.90 (61271 hom., cov: 30)
• Consequence: PTGER3 NM_198714.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0720
• Publications: 7 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]

PTGER3-AS1 (HGNC:40481):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198714.2. 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
	PTGER3	NM_198714.2		c.*23+24763A>G		intron	N/A	NP_942007.1	P43115-1
	PTGER3	NM_198716.2		c.1104+24763A>G		intron	N/A	NP_942009.1	P43115-4
	PTGER3	NM_198717.2		c.1078-76141A>G		intron	N/A	NP_942010.1	P43115-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTGER3	ENST00000370931.7	TSL:1	c.*23+24763A>G		intron	N/A	ENSP00000359969.3	P43115-1
	PTGER3	ENST00000460330.5	TSL:1	c.1104+24763A>G		intron	N/A	ENSP00000418073.1	P43115-4
	PTGER3	ENST00000628037.2	TSL:1	c.1078-76141A>G		intron	N/A	ENSP00000486617.1	P43115-3

Frequencies

GnomAD3 genomes AF: 0.896 AC: 136186 AN: 152016 Hom.: 61202 Cov.: 30

Gnomad AFR AF: 0.971

Gnomad AMI AF: 0.874

Gnomad AMR AF: 0.909

Gnomad ASJ AF: 0.864

Gnomad EAS AF: 0.932

Gnomad SAS AF: 0.857

Gnomad FIN AF: 0.884

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.850

Gnomad OTH AF: 0.904

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

GnomAD4 genome AF: 0.896 AC: 136315 AN: 152134 Hom.: 61271 Cov.: 30 AF XY: 0.898 AC XY: 66758 AN XY: 74332

African (AFR) AF: 0.972 AC: 40361 AN: 41542

American (AMR) AF: 0.909 AC: 13864 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.864 AC: 3001 AN: 3472

East Asian (EAS) AF: 0.932 AC: 4799 AN: 5148

South Asian (SAS) AF: 0.858 AC: 4134 AN: 4816

European-Finnish (FIN) AF: 0.884 AC: 9336 AN: 10564

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.850 AC: 57841 AN: 68016

Other (OTH) AF: 0.905 AC: 1913 AN: 2114

Alfa AF: 0.866 Hom.: 123950

Bravo AF: 0.902

Asia WGS AF: 0.919 AC: 3195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	6.7
DANN	Benign	0.36
PhyloP100		0.072
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs578096; hg19: chr1-71394683;