Variant rs34497267 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.30G>A(p.Val10Val) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 1,542,620 control chromosomes in the GnomAD database, including 9,947 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 0.087 ( 717 hom., cov: 34)

Exomes 𝑓: 0.11 ( 9230 hom. )

Consequence

GPER1
NM_001098201.3 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.20

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:

C7orf50 (HGNC:):

C7orf50 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP7

Synonymous conserved (PhyloP=-2.2 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.112 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GPER1	NM_001098201.3 linkuse as main transcript	c.30G>A	p.Val10Val	synonymous_variant	2/2	ENST00000397088.4	NP_001091671.1	Q99527A0A024R849
C7orf50	NM_001318252.2 linkuse as main transcript	c.129+35499C>T		intron_variant		ENST00000397098.8	NP_001305181.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GPER1	ENST00000397088.4 linkuse as main transcript	c.30G>A	p.Val10Val	synonymous_variant	2/2	1	NM_001098201.3	ENSP00000380277.3		Q99527
C7orf50	ENST00000397098.8 linkuse as main transcript	c.129+35499C>T		intron_variant		1	NM_001318252.2	ENSP00000380286.3		Q9BRJ6

Frequencies

GnomAD3 genomes

AF:

0.0867

AC:

13191

AN:

152186

Hom.:

716

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0346

Gnomad AMI

AF:

0.163

Gnomad AMR

AF:

0.0932

Gnomad ASJ

AF:

0.141

Gnomad EAS

AF:

0.0535

Gnomad SAS

AF:

0.114

Gnomad FIN

AF:

0.0808

Gnomad MID

AF:

0.0538

Gnomad NFE

AF:

0.115

Gnomad OTH

AF:

0.0931

GnomAD3 exomes

AF:

0.0955

AC:

19222

AN:

201364

Hom.:

1063

AF XY:

0.0982

AC XY:

10507

AN XY:

106984

show subpopulations

Gnomad AFR exome

AF:

0.0331

Gnomad AMR exome

AF:

0.0847

Gnomad ASJ exome

AF:

0.146

Gnomad EAS exome

AF:

0.0419

Gnomad SAS exome

AF:

0.125

Gnomad FIN exome

AF:

0.0844

Gnomad NFE exome

AF:

0.111

Gnomad OTH exome

AF:

0.110

GnomAD4 exome

AF:

0.112

AC:

156252

AN:

1390316

Hom.:

9230

Cov.:

AF XY:

0.112

AC XY:

76581

AN XY:

683034

show subpopulations

Gnomad4 AFR exome

AF:

0.0292

Gnomad4 AMR exome

AF:

0.0856

Gnomad4 ASJ exome

AF:

0.144

Gnomad4 EAS exome

AF:

0.0393

Gnomad4 SAS exome

AF:

0.121

Gnomad4 FIN exome

AF:

0.0848

Gnomad4 NFE exome

AF:

0.119

Gnomad4 OTH exome

AF:

0.109

GnomAD4 genome

AF:

0.0866

AC:

13196

AN:

152304

Hom.:

717

Cov.:

AF XY:

0.0854

AC XY:

6359

AN XY:

74464

show subpopulations

Gnomad4 AFR

AF:

0.0346

Gnomad4 AMR

AF:

0.0934

Gnomad4 ASJ

AF:

0.141

Gnomad4 EAS

AF:

0.0534

Gnomad4 SAS

AF:

0.114

Gnomad4 FIN

AF:

0.0808

Gnomad4 NFE

AF:

0.115

Gnomad4 OTH

AF:

0.0945

Alfa

AF:

0.0998

Hom.:

334

Bravo

AF:

0.0830

Asia WGS

AF:

0.102

AC:

353

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.039

DANN

Benign

0.58

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.8

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