rs1133043

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001098201.3(GPER1):​c.*813C>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 0.0000617 in 469,982 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.00013 ( 0 hom., cov: 34)
Exomes 𝑓: 0.000028 ( 0 hom. )

Consequence

GPER1
NM_001098201.3 3_prime_UTR

Scores

10

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

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.031781107).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
GPER1NM_001098201.3 linkuse as main transcriptc.*813C>A 3_prime_UTR_variant 2/2 ENST00000397088.4
C7orf50NM_001318252.2 linkuse as main transcriptc.129+33588G>T intron_variant ENST00000397098.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
GPER1ENST00000397088.4 linkuse as main transcriptc.*813C>A 3_prime_UTR_variant 2/21 NM_001098201.3 P1
C7orf50ENST00000397098.8 linkuse as main transcriptc.129+33588G>T intron_variant 1 NM_001318252.2 P1

Frequencies

GnomAD3 genomes
AF:
0.000118
AC:
18
AN:
152108
Hom.:
0
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.000386
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000207
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000147
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000462
AC:
7
AN:
151652
Hom.:
0
AF XY:
0.0000369
AC XY:
3
AN XY:
81310
show subpopulations
Gnomad AFR exome
AF:
0.000587
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000133
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000283
AC:
9
AN:
317756
Hom.:
0
Cov.:
0
AF XY:
0.0000335
AC XY:
6
AN XY:
179300
show subpopulations
Gnomad4 AFR exome
AF:
0.000464
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000502
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.000140
GnomAD4 genome
AF:
0.000131
AC:
20
AN:
152226
Hom.:
0
Cov.:
34
AF XY:
0.000107
AC XY:
8
AN XY:
74422
show subpopulations
Gnomad4 AFR
AF:
0.000433
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000207
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000147
Gnomad4 OTH
AF:
0.00
ExAC
AF:
0.0000967
AC:
2

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.66
T
BayesDel_noAF
Benign
-0.86
CADD
Benign
0.90
DANN
Benign
0.23
Eigen
Benign
-0.84
Eigen_PC
Benign
-1.0
FATHMM_MKL
Benign
0.0098
N
LIST_S2
Benign
0.16
T
MetaRNN
Benign
0.032
T
MetaSVM
Benign
-0.93
T
MutationTaster
Benign
1.0
P;P;P;P;P;P
Vest4
0.12
MVP
0.043
ClinPred
0.079
T
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.

Other links and lift over

dbSNP: rs1133043; hg19: chr7-1133305; API