rs10483774
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001291712.2(ESR2):c.-91+652C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0164 in 152,304 control chromosomes in the GnomAD database, including 70 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 0.016 ( 70 hom., cov: 32)
Consequence
ESR2
NM_001291712.2 intron
NM_001291712.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.251
Genes affected
ESR2 (HGNC:3468): (estrogen receptor 2) This gene encodes a member of the family of estrogen receptors and superfamily of nuclear receptor transcription factors. The gene product contains an N-terminal DNA binding domain and C-terminal ligand binding domain and is localized to the nucleus, cytoplasm, and mitochondria. Upon binding to 17beta-estradiol or related ligands, the encoded protein forms homo- or hetero-dimers that interact with specific DNA sequences to activate transcription. Some isoforms dominantly inhibit the activity of other estrogen receptor family members. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been fully characterized. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0798 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ESR2 | NM_001291712.2 | c.-91+652C>T | intron_variant | Intron 6 of 13 | NP_001278641.1 | |||
ESR2 | NM_001291723.1 | c.-90-13806C>T | intron_variant | Intron 1 of 8 | NP_001278652.1 | |||
ESR2 | XM_047431076.1 | c.-90-13806C>T | intron_variant | Intron 2 of 9 | XP_047287032.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0163 AC: 2485AN: 152186Hom.: 69 Cov.: 32 show subpopulations
GnomAD3 genomes
AF:
AC:
2485
AN:
152186
Hom.:
Cov.:
32
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:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0164 AC: 2495AN: 152304Hom.: 70 Cov.: 32 AF XY: 0.0172 AC XY: 1281AN XY: 74476 show subpopulations
GnomAD4 genome
AF:
AC:
2495
AN:
152304
Hom.:
Cov.:
32
AF XY:
AC XY:
1281
AN XY:
74476
Gnomad4 AFR
AF:
AC:
0.0229766
AN:
0.0229766
Gnomad4 AMR
AF:
AC:
0.0600575
AN:
0.0600575
Gnomad4 ASJ
AF:
AC:
0.00115207
AN:
0.00115207
Gnomad4 EAS
AF:
AC:
0.0864198
AN:
0.0864198
Gnomad4 SAS
AF:
AC:
0.00186722
AN:
0.00186722
Gnomad4 FIN
AF:
AC:
0.00546139
AN:
0.00546139
Gnomad4 NFE
AF:
AC:
0.000646831
AN:
0.000646831
Gnomad4 OTH
AF:
AC:
0.0265152
AN:
0.0265152
Heterozygous variant carriers
0
116
233
349
466
582
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
30
60
90
120
150
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
123
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
Mutation Taster
=100/0
polymorphism (auto)
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at