rs977214

Variant names:

• chr1-70960577-A-G
• rs977214
• ENST00000356595.8:c.1078-6788T>C

Variant summary

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

The ENST00000356595.8(PTGER3):​c.1078-6788T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.132 in 152,128 control chromosomes in the GnomAD database, including 2,068 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 (2068 hom., cov: 32)
• Consequence: PTGER3 ENST00000356595.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.25
• 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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.271 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PTGER3	NM_198718.2	c.1078-6788T>C		intron_variant	Intron 2 of 3		NP_942011.1
PTGER3	NM_001126044.2	c.1170-6788T>C		intron_variant	Intron 3 of 4		NP_001119516.1
PTGER3	NM_198714.2	c.1170-6788T>C		intron_variant	Intron 3 of 4		NP_942007.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PTGER3	ENST00000356595.8	c.1078-6788T>C		intron_variant	Intron 2 of 3	1		ENSP00000349003.4
PTGER3	ENST00000370931.7	c.1170-6788T>C		intron_variant	Intron 3 of 4	1		ENSP00000359969.3
PTGER3	ENST00000460330.5	c.1078-6788T>C		intron_variant	Intron 2 of 3	1		ENSP00000418073.1

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20084 AN: 152010 Hom.: 2058 Cov.: 32

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.0775

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.000964

Gnomad SAS AF: 0.0242

Gnomad FIN AF: 0.0502

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.0892

Gnomad OTH AF: 0.133

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

GnomAD4 genome AF: 0.132 AC: 20127 AN: 152128 Hom.: 2068 Cov.: 32 AF XY: 0.128 AC XY: 9514 AN XY: 74378

African (AFR) AF: 0.276 AC: 11415 AN: 41428

American (AMR) AF: 0.0773 AC: 1181 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.108 AC: 374 AN: 3468

East Asian (EAS) AF: 0.000966 AC: 5 AN: 5174

South Asian (SAS) AF: 0.0245 AC: 118 AN: 4822

European-Finnish (FIN) AF: 0.0502 AC: 533 AN: 10616

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.0892 AC: 6070 AN: 68016

Other (OTH) AF: 0.132 AC: 279 AN: 2116

Alfa AF: 0.107 Hom.: 3553

Bravo AF: 0.141

Asia WGS AF: 0.0310 AC: 107 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	5.5
DANN	Benign	0.67
PhyloP100		2.2
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: rs977214; hg19: chr1-71426260;