Variant chr7-1091720-T-C details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000397088.4(GPER1):c.-9T>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.625 in 1,514,496 control chromosomes in the GnomAD database, including 298,678 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 0.67 ( 34416 hom., cov: 34)

Exomes 𝑓: 0.62 ( 264262 hom. )

Consequence

GPER1
ENST00000397088.4 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.69

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 (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.789 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.-9T>C		5_prime_UTR_variant	2/2	ENST00000397088.4	NP_001091671.1
C7orf50	NM_001318252.2 linkuse as main transcript	c.129+35537A>G		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.-9T>C		5_prime_UTR_variant	2/2	1	NM_001098201.3	ENSP00000380277	P1
C7orf50	ENST00000397098.8 linkuse as main transcript	c.129+35537A>G		intron_variant		1	NM_001318252.2	ENSP00000380286	P1

Frequencies

GnomAD3 genomes

AF:

0.665

AC:

101140

AN:

152036

Hom.:

34376

Cov.:

show subpopulations

Gnomad AFR

AF:

0.797

Gnomad AMI

AF:

0.666

Gnomad AMR

AF:

0.635

Gnomad ASJ

AF:

0.624

Gnomad EAS

AF:

0.424

Gnomad SAS

AF:

0.580

Gnomad FIN

AF:

0.640

Gnomad MID

AF:

0.652

Gnomad NFE

AF:

0.623

Gnomad OTH

AF:

0.640

GnomAD3 exomes

AF:

0.620

AC:

113415

AN:

182798

Hom.:

35910

AF XY:

0.615

AC XY:

59204

AN XY:

96228

show subpopulations

Gnomad AFR exome

AF:

0.801

Gnomad AMR exome

AF:

0.662

Gnomad ASJ exome

AF:

0.629

Gnomad EAS exome

AF:

0.409

Gnomad SAS exome

AF:

0.596

Gnomad FIN exome

AF:

0.645

Gnomad NFE exome

AF:

0.616

Gnomad OTH exome

AF:

0.615

GnomAD4 exome

AF:

0.620

AC:

845122

AN:

1362342

Hom.:

264262

Cov.:

AF XY:

0.619

AC XY:

413524

AN XY:

667922

show subpopulations

Gnomad4 AFR exome

AF:

0.808

Gnomad4 AMR exome

AF:

0.658

Gnomad4 ASJ exome

AF:

0.625

Gnomad4 EAS exome

AF:

0.504

Gnomad4 SAS exome

AF:

0.598

Gnomad4 FIN exome

AF:

0.643

Gnomad4 NFE exome

AF:

0.619

Gnomad4 OTH exome

AF:

0.614

GnomAD4 genome

AF:

0.665

AC:

101225

AN:

152154

Hom.:

34416

Cov.:

AF XY:

0.662

AC XY:

49214

AN XY:

74358

show subpopulations

Gnomad4 AFR

AF:

0.797

Gnomad4 AMR

AF:

0.635

Gnomad4 ASJ

AF:

0.624

Gnomad4 EAS

AF:

0.423

Gnomad4 SAS

AF:

0.581

Gnomad4 FIN

AF:

0.640

Gnomad4 NFE

AF:

0.623

Gnomad4 OTH

AF:

0.636

Alfa

AF:

0.625

Hom.:

39174

Bravo

AF:

0.669

Asia WGS

AF:

0.527

AC:

1831

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.037

DANN

Benign

0.31

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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