chr7-1093535-G-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001098201.3(GPER1):c.*679G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 470,740 control chromosomes in the GnomAD database, including 8,508 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 0.21 ( 4318 hom., cov: 33)
Exomes 𝑓: 0.15 ( 4190 hom. )
Consequence
GPER1
NM_001098201.3 3_prime_UTR
NM_001098201.3 3_prime_UTR
Scores
10
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -2.08
Publications
13 publications found
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]
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.0024252534).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GPER1 | NM_001098201.3 | c.*679G>T | 3_prime_UTR_variant | Exon 2 of 2 | ENST00000397088.4 | NP_001091671.1 | ||
CHLSN | NM_001318252.2 | c.129+33722C>A | intron_variant | Intron 2 of 4 | ENST00000397098.8 | NP_001305181.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GPER1 | ENST00000397088.4 | c.*679G>T | 3_prime_UTR_variant | Exon 2 of 2 | 1 | NM_001098201.3 | ENSP00000380277.3 | |||
C7orf50 | ENST00000397098.8 | c.129+33722C>A | intron_variant | Intron 2 of 4 | 1 | NM_001318252.2 | ENSP00000380286.3 |
Frequencies
GnomAD3 genomes AF: 0.211 AC: 32088AN: 151998Hom.: 4309 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
32088
AN:
151998
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD2 exomes AF: 0.149 AC: 22478AN: 151050 AF XY: 0.149 show subpopulations
GnomAD2 exomes
AF:
AC:
22478
AN:
151050
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.152 AC: 48315AN: 318624Hom.: 4190 Cov.: 0 AF XY: 0.153 AC XY: 27522AN XY: 180000 show subpopulations
GnomAD4 exome
AF:
AC:
48315
AN:
318624
Hom.:
Cov.:
0
AF XY:
AC XY:
27522
AN XY:
180000
show subpopulations
African (AFR)
AF:
AC:
3393
AN:
8632
American (AMR)
AF:
AC:
3259
AN:
27286
Ashkenazi Jewish (ASJ)
AF:
AC:
1842
AN:
10790
East Asian (EAS)
AF:
AC:
632
AN:
9214
South Asian (SAS)
AF:
AC:
9326
AN:
59742
European-Finnish (FIN)
AF:
AC:
3109
AN:
26834
Middle Eastern (MID)
AF:
AC:
328
AN:
2776
European-Non Finnish (NFE)
AF:
AC:
24068
AN:
159028
Other (OTH)
AF:
AC:
2358
AN:
14322
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.491
Heterozygous variant carriers
0
2900
5800
8701
11601
14501
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome AF: 0.211 AC: 32129AN: 152116Hom.: 4318 Cov.: 33 AF XY: 0.206 AC XY: 15359AN XY: 74380 show subpopulations
GnomAD4 genome
AF:
AC:
32129
AN:
152116
Hom.:
Cov.:
33
AF XY:
AC XY:
15359
AN XY:
74380
show subpopulations
African (AFR)
AF:
AC:
15949
AN:
41474
American (AMR)
AF:
AC:
2402
AN:
15276
Ashkenazi Jewish (ASJ)
AF:
AC:
596
AN:
3464
East Asian (EAS)
AF:
AC:
402
AN:
5166
South Asian (SAS)
AF:
AC:
712
AN:
4822
European-Finnish (FIN)
AF:
AC:
1192
AN:
10594
Middle Eastern (MID)
AF:
AC:
45
AN:
292
European-Non Finnish (NFE)
AF:
AC:
10244
AN:
68000
Other (OTH)
AF:
AC:
436
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1227
2454
3680
4907
6134
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
TwinsUK
AF:
AC:
552
ALSPAC
AF:
AC:
617
ExAC
AF:
AC:
2886
Asia WGS
AF:
AC:
514
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
PhyloP100
Vest4
ClinPred
T
GERP RS
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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