Variant 7-1093669-C-G 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.*813C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.626 in 469,890 control chromosomes in the GnomAD database, including 93,478 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 0.65 ( 32780 hom., cov: 34)

Exomes 𝑓: 0.61 ( 60698 hom. )

Consequence

GPER1
NM_001098201.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.76

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=1.6484207E-6).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.744 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.*813C>G		3_prime_UTR_variant	2/2	ENST00000397088.4
C7orf50	NM_001318252.2 linkuse as main transcript	c.129+33588G>C		intron_variant		ENST00000397098.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPER1	ENST00000397088.4 linkuse as main transcript	c.*813C>G		3_prime_UTR_variant	2/2	1	NM_001098201.3	P1
C7orf50	ENST00000397098.8 linkuse as main transcript	c.129+33588G>C		intron_variant		1	NM_001318252.2	P1

Frequencies

GnomAD3 genomes

AF:

0.651

AC:

98932

AN:

152076

Hom.:

32745

Cov.:

show subpopulations

Gnomad AFR

AF:

0.751

Gnomad AMI

AF:

0.650

Gnomad AMR

AF:

0.615

Gnomad ASJ

AF:

0.624

Gnomad EAS

AF:

0.409

Gnomad SAS

AF:

0.555

Gnomad FIN

AF:

0.641

Gnomad MID

AF:

0.646

Gnomad NFE

AF:

0.626

Gnomad OTH

AF:

0.625

GnomAD3 exomes

AF:

0.607

AC:

92084

AN:

151652

Hom.:

28474

AF XY:

0.604

AC XY:

49144

AN XY:

81310

show subpopulations

Gnomad AFR exome

AF:

0.753

Gnomad AMR exome

AF:

0.627

Gnomad ASJ exome

AF:

0.632

Gnomad EAS exome

AF:

0.381

Gnomad SAS exome

AF:

0.576

Gnomad FIN exome

AF:

0.647

Gnomad NFE exome

AF:

0.621

Gnomad OTH exome

AF:

0.599

GnomAD4 exome

AF:

0.615

AC:

195369

AN:

317696

Hom.:

60698

Cov.:

AF XY:

0.611

AC XY:

109509

AN XY:

179260

show subpopulations

Gnomad4 AFR exome

AF:

0.752

Gnomad4 AMR exome

AF:

0.629

Gnomad4 ASJ exome

AF:

0.631

Gnomad4 EAS exome

AF:

0.409

Gnomad4 SAS exome

AF:

0.580

Gnomad4 FIN exome

AF:

0.645

Gnomad4 NFE exome

AF:

0.624

Gnomad4 OTH exome

AF:

0.614

GnomAD4 genome

AF:

0.651

AC:

99009

AN:

152194

Hom.:

32780

Cov.:

AF XY:

0.647

AC XY:

48124

AN XY:

74404

show subpopulations

Gnomad4 AFR

AF:

0.751

Gnomad4 AMR

AF:

0.615

Gnomad4 ASJ

AF:

0.624

Gnomad4 EAS

AF:

0.408

Gnomad4 SAS

AF:

0.556

Gnomad4 FIN

AF:

0.641

Gnomad4 NFE

AF:

0.626

Gnomad4 OTH

AF:

0.622

Alfa

AF:

0.588

Hom.:

3343

Bravo

AF:

0.651

TwinsUK

AF:

0.616

AC:

2283

ALSPAC

AF:

0.619

AC:

2385

ExAC

AF:

0.583

AC:

12060

Asia WGS

AF:

0.508

AC:

1765

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.89

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.96

DANN

Benign

0.43

Eigen

Benign

-0.84

Eigen_PC

Benign

-1.0

FATHMM_MKL

Benign

0.0028

LIST_S2

Benign

0.21

MetaRNN

Benign

0.0000016

MetaSVM

Benign

-1.0

MutationTaster

Benign

1.0

P;P;P;P;P;P

Vest4

0.057

ClinPred

0.0043

GERP RS

-0.41

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