Variant rs10235056 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001098201.3(GPER1):c.*256G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0809 in 652,682 control chromosomes in the GnomAD database, including 2,447 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 0.081 ( 551 hom., cov: 33)

Exomes 𝑓: 0.081 ( 1896 hom. )

Consequence

GPER1
NM_001098201.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.209

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 -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0016965866).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.107 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.*256G>A		3_prime_UTR_variant	2/2	ENST00000397088.4
C7orf50	NM_001318252.2 linkuse as main transcript	c.129+34145C>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.*256G>A		3_prime_UTR_variant	2/2	1	NM_001098201.3	P1
C7orf50	ENST00000397098.8 linkuse as main transcript	c.129+34145C>T		intron_variant		1	NM_001318252.2	P1

Frequencies

GnomAD3 genomes

AF:

0.0810

AC:

12321

AN:

152020

Hom.:

549

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0703

Gnomad AMI

AF:

0.141

Gnomad AMR

AF:

0.112

Gnomad ASJ

AF:

0.0695

Gnomad EAS

AF:

0.0256

Gnomad SAS

AF:

0.0664

Gnomad FIN

AF:

0.0547

Gnomad MID

AF:

0.0854

Gnomad NFE

AF:

0.0898

Gnomad OTH

AF:

0.0794

GnomAD3 exomes

AF:

0.0822

AC:

12068

AN:

146790

Hom.:

617

AF XY:

0.0811

AC XY:

6427

AN XY:

79242

show subpopulations

Gnomad AFR exome

AF:

0.0713

Gnomad AMR exome

AF:

0.120

Gnomad ASJ exome

AF:

0.0740

Gnomad EAS exome

AF:

0.0222

Gnomad SAS exome

AF:

0.0688

Gnomad FIN exome

AF:

0.0602

Gnomad NFE exome

AF:

0.0899

Gnomad OTH exome

AF:

0.0813

GnomAD4 exome

AF:

0.0808

AC:

40461

AN:

500544

Hom.:

1896

Cov.:

AF XY:

0.0803

AC XY:

21816

AN XY:

271644

show subpopulations

Gnomad4 AFR exome

AF:

0.0697

Gnomad4 AMR exome

AF:

0.119

Gnomad4 ASJ exome

AF:

0.0715

Gnomad4 EAS exome

AF:

0.0207

Gnomad4 SAS exome

AF:

0.0702

Gnomad4 FIN exome

AF:

0.0592

Gnomad4 NFE exome

AF:

0.0880

Gnomad4 OTH exome

AF:

0.0822

GnomAD4 genome

AF:

0.0811

AC:

12333

AN:

152138

Hom.:

551

Cov.:

AF XY:

0.0794

AC XY:

5907

AN XY:

74372

show subpopulations

Gnomad4 AFR

AF:

0.0704

Gnomad4 AMR

AF:

0.112

Gnomad4 ASJ

AF:

0.0695

Gnomad4 EAS

AF:

0.0253

Gnomad4 SAS

AF:

0.0667

Gnomad4 FIN

AF:

0.0547

Gnomad4 NFE

AF:

0.0899

Gnomad4 OTH

AF:

0.0795

Alfa

AF:

0.0911

Hom.:

270

Bravo

AF:

0.0844

TwinsUK

AF:

0.0965

AC:

358

ALSPAC

AF:

0.0833

AC:

321

ExAC

AF:

0.0509

AC:

1487

Asia WGS

AF:

0.0520

AC:

180

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.81

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.34

DANN

Benign

0.49

DEOGEN2

Benign

0.014

T;.

Eigen

Benign

-1.0

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.071

LIST_S2

Benign

0.35

T;T

MetaRNN

Benign

0.0017

T;T

MetaSVM

Benign

-1.0

MutationTaster

Benign

1.0

N;N;N;N;N;N

Sift4G

Pathogenic

0.0

D;D

Vest4

0.086

ClinPred

0.0018

GERP RS

-2.1

RBP_binding_hub_radar

0.97

RBP_regulation_power_radar

2.3

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