Variant rs3808352 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001098201.3(GPER1):c.789G>A(p.Ala263=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.172 in 1,607,768 control chromosomes in the GnomAD database, including 25,073 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 0.14 ( 1777 hom., cov: 33)

Exomes 𝑓: 0.18 ( 23296 hom. )

Consequence

GPER1
NM_001098201.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -4.47

Variant links:

Genes affected

GPER1 (HGNC:4485): (G protein-coupled estrogen receptor 1) This gene encodes a multi-pass membrane protein that localizes to the endoplasmic reticulum and a member of the G-protein coupled receptor 1 family. This receptor binds estrogen and activates multiple downstream signaling pathways, leading to stimulation of adenylate cyclase and an increase in cyclic AMP levels, while also promoting intracellular calcium mobilization and synthesis of phosphatidylinositol 3,4,5-trisphosphate in the nucleus. This protein therefore plays a role in the rapid nongenomic signaling events widely observed following stimulation of cells and tissues with estrogen. This receptor has been shown to play a role in diverse biological processes, including bone and nervous system development, metabolism, cognition, male fertility and uterine function. [provided by RefSeq, Aug 2017]

GPER1 links:

C7orf50 (HGNC:22421): (chromosome 7 open reading frame 50) Enables RNA binding activity. [provided by Alliance of Genome Resources, Apr 2022]

C7orf50 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BP7

Synonymous conserved (PhyloP=-4.47 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.186 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GPER1	NM_001098201.3 linkuse as main transcript	c.789G>A	p.Ala263=	synonymous_variant	2/2	ENST00000397088.4
C7orf50	NM_001318252.2 linkuse as main transcript	c.129+34740C>T		intron_variant		ENST00000397098.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPER1	ENST00000397088.4 linkuse as main transcript	c.789G>A	p.Ala263=	synonymous_variant	2/2	1	NM_001098201.3	P1
C7orf50	ENST00000397098.8 linkuse as main transcript	c.129+34740C>T		intron_variant		1	NM_001318252.2	P1

Frequencies

GnomAD3 genomes

AF:

0.138

AC:

21045

AN:

152128

Hom.:

1776

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0489

Gnomad AMI

AF:

0.228

Gnomad AMR

AF:

0.142

Gnomad ASJ

AF:

0.236

Gnomad EAS

AF:

0.0892

Gnomad SAS

AF:

0.145

Gnomad FIN

AF:

0.140

Gnomad MID

AF:

0.149

Gnomad NFE

AF:

0.188

Gnomad OTH

AF:

0.148

GnomAD3 exomes

AF:

0.155

AC:

38019

AN:

245648

Hom.:

3282

AF XY:

0.159

AC XY:

21172

AN XY:

133424

show subpopulations

Gnomad AFR exome

AF:

0.0475

Gnomad AMR exome

AF:

0.119

Gnomad ASJ exome

AF:

0.241

Gnomad EAS exome

AF:

0.0720

Gnomad SAS exome

AF:

0.158

Gnomad FIN exome

AF:

0.147

Gnomad NFE exome

AF:

0.186

Gnomad OTH exome

AF:

0.175

GnomAD4 exome

AF:

0.175

AC:

254802

AN:

1455522

Hom.:

23296

Cov.:

AF XY:

0.175

AC XY:

126526

AN XY:

724362

show subpopulations

Gnomad4 AFR exome

AF:

0.0435

Gnomad4 AMR exome

AF:

0.123

Gnomad4 ASJ exome

AF:

0.239

Gnomad4 EAS exome

AF:

0.0840

Gnomad4 SAS exome

AF:

0.156

Gnomad4 FIN exome

AF:

0.146

Gnomad4 NFE exome

AF:

0.186

Gnomad4 OTH exome

AF:

0.172

GnomAD4 genome

AF:

0.138

AC:

21043

AN:

152246

Hom.:

1777

Cov.:

AF XY:

0.137

AC XY:

10184

AN XY:

74438

show subpopulations

Gnomad4 AFR

AF:

0.0487

Gnomad4 AMR

AF:

0.142

Gnomad4 ASJ

AF:

0.236

Gnomad4 EAS

AF:

0.0888

Gnomad4 SAS

AF:

0.146

Gnomad4 FIN

AF:

0.140

Gnomad4 NFE

AF:

0.188

Gnomad4 OTH

AF:

0.147

Alfa

AF:

0.158

Hom.:

960

Bravo

AF:

0.133

Asia WGS

AF:

0.126

AC:

439

AN:

3478

EpiCase

AF:

0.189

EpiControl

AF:

0.185

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.20

DANN

Benign

0.93

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over