1-70953784-T-C

Variant names:

• chr1-70953784-T-C
• rs761024899
• ENST00000356595.8:c.1083A>G

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_198718.2(PTGER3):​c.1083A>G​(p.Arg361Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000794 in 1,260,078 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 7.9e-7 (0 hom.)
• Consequence: PTGER3 NM_198718.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.971
• Publications: 0 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: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BP7: Synonymous conserved (PhyloP=-0.971 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198718.2. 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_198718.2		c.1083A>G	p.Arg361Arg	synonymous	Exon 3 of 4	NP_942011.1	P43115-5
	PTGER3	NM_198716.2		c.1083A>G	p.Arg361Arg	synonymous	Exon 3 of 4	NP_942009.1	P43115-4
	PTGER3	NM_001126044.2		c.*2A>G		3_prime_UTR	Exon 4 of 5	NP_001119516.1	P43115-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PTGER3	ENST00000356595.8	TSL:1	c.1083A>G	p.Arg361Arg	synonymous	Exon 3 of 4	ENSP00000349003.4	P43115-5
	PTGER3	ENST00000460330.5	TSL:1	c.1083A>G	p.Arg361Arg	synonymous	Exon 3 of 4	ENSP00000418073.1	P43115-4
	PTGER3	ENST00000370931.7	TSL:1	c.*2A>G		3_prime_UTR	Exon 4 of 5	ENSP00000359969.3	P43115-1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 7.94e-7 AC: 1 AN: 1260078 Hom.: 0 Cov.: 18 AF XY: 0.00 AC XY: 0 AN XY: 625320

African (AFR) AF: 0.00 AC: 0 AN: 25952

American (AMR) AF: 0.0000449 AC: 1 AN: 22290

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 21338

East Asian (EAS) AF: 0.00 AC: 0 AN: 33126

South Asian (SAS) AF: 0.00 AC: 0 AN: 68644

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 47376

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5188

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 983402

Other (OTH) AF: 0.00 AC: 0 AN: 52762

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.62
DANN	Benign	0.79
PhyloP100		-0.97
Mutation Taster		=100/0	polymorphism

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs761024899; hg19: chr1-71419467;