chr14:64233098:C>T Detail (hg38) (ESR2)

Information

Genome

Assembly Position
hg19 chr14:64,699,816-64,699,816 View the variant detail on this assembly version.
hg38 chr14:64,233,098-64,233,098

HGVS

Type Transcript Protein
RefSeq NM_001271877.1:c.*39G>A
NM_001437.2:c.*39G>A
NM_001040275.1:c.1406+1872G>A
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:0.149
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.111

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 601663 OMIM
HGNC 3468 HGNC
Ensembl ENSG00000140009 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv51068648 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2018-07-09 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.008 gynecomastia Thus, the aim of this study was to evaluate the relationships between CYP19 (rs2... BeFree 24625355 Detail
<0.001 gynecomastia Thus, the aim of this study was to evaluate the relationships between CYP19 (rs2... BeFree 24625355 Detail
0.003 low tension glaucoma Four hundred and twenty-five Japanese patients with POAG, including normal-tensi... BeFree 20399928 Detail
0.030 breast carcinoma The ESR2 rs4986938 and rs1256049 polymorphisms were described to present associa... BeFree 25341980 Detail
0.068 Malignant neoplasm of breast The ESR2 rs4986938 and rs1256049 polymorphisms were described to present associa... BeFree 25341980 Detail
0.087 obesity The relationship of three polymorphisms (rs1271572, rs1256049 and rs4986938) and... BeFree 19111408 Detail
<0.001 HIV Infections To investigate genetic single nucleotide polymorphisms (SNPs) in estrogen recept... BeFree 22011627 Detail
0.003 Metabolic syndrome X To investigate genetic single nucleotide polymorphisms (SNPs) in estrogen recept... BeFree 22011627 Detail
0.007 Metabolic syndrome X To investigate genetic single nucleotide polymorphisms (SNPs) in estrogen recept... BeFree 22011627 Detail
<0.001 HIV Infections To investigate genetic single nucleotide polymorphisms (SNPs) in estrogen recept... BeFree 22011627 Detail
<0.001 Mental Depression In men, only the ER-β rs4986938 polymorphism showed a weak association with depr... BeFree 21804148 Detail
<0.001 bile duct carcinoma Also, the ESR2 rs4986938 (38 bp 3' of STP) GG genotype was associated with a hig... BeFree 20172949 Detail
0.149 endometriosis To investigate whether a polymorphism in the ESR2 gene (rs4986938, previously as... BeFree 17941906 Detail
0.003 Graves Disease The association between rs4986938 (ESR2) and aSLE is a novel finding, consistent... BeFree 20961965 Detail
<0.001 hepatitis C We provide here the first report that rs4986938 in the ESR2 gene played a potent... BeFree 25261585 Detail
0.005 Coronary Arteriosclerosis To investigate whether a polymorphism in the ESR2 gene (rs4986938, previously as... BeFree 17941906 Detail
0.008 Malignant neoplasm of prostate However, an interactive association with BMI was observed in the relationship be... BeFree 19654868 Detail
0.001 prostate carcinoma However, an interactive association with BMI was observed in the relationship be... BeFree 19654868 Detail
<0.001 bile duct carcinoma Also, the ESR2 rs4986938 (38 bp 3' of STP) GG genotype was associated with a hig... BeFree 20172949 Detail
0.081 depressive disorder In men, only the ER-β rs4986938 polymorphism showed a weak association with depr... BeFree 21804148 Detail
0.123 Coronary heart disease To investigate whether a polymorphism in the ESR2 gene (rs4986938, previously as... BeFree 17941906 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_001437.3(ESR2):c.*39G>A AND not provided ClinVar Detail
Thus, the aim of this study was to evaluate the relationships between CYP19 (rs2414096), ER alpha (r... DisGeNET Detail
Thus, the aim of this study was to evaluate the relationships between CYP19 (rs2414096), ER alpha (r... DisGeNET Detail
Four hundred and twenty-five Japanese patients with POAG, including normal-tension glaucoma (NTG, n ... DisGeNET Detail
The ESR2 rs4986938 and rs1256049 polymorphisms were described to present association with breast can... DisGeNET Detail
The ESR2 rs4986938 and rs1256049 polymorphisms were described to present association with breast can... DisGeNET Detail
The relationship of three polymorphisms (rs1271572, rs1256049 and rs4986938) and their associated ha... DisGeNET Detail
To investigate genetic single nucleotide polymorphisms (SNPs) in estrogen receptor-α (ERα) (ESR1, rs... DisGeNET Detail
To investigate genetic single nucleotide polymorphisms (SNPs) in estrogen receptor-α (ERα) (ESR1, rs... DisGeNET Detail
To investigate genetic single nucleotide polymorphisms (SNPs) in estrogen receptor-α (ERα) (ESR1, rs... DisGeNET Detail
To investigate genetic single nucleotide polymorphisms (SNPs) in estrogen receptor-α (ERα) (ESR1, rs... DisGeNET Detail
In men, only the ER-β rs4986938 polymorphism showed a weak association with depression risk. DisGeNET Detail
Also, the ESR2 rs4986938 (38 bp 3' of STP) GG genotype was associated with a higher risk of bile duc... DisGeNET Detail
To investigate whether a polymorphism in the ESR2 gene (rs4986938, previously associated with endome... DisGeNET Detail
The association between rs4986938 (ESR2) and aSLE is a novel finding, consistent with our recent rep... DisGeNET Detail
We provide here the first report that rs4986938 in the ESR2 gene played a potential sex-specific rol... DisGeNET Detail
To investigate whether a polymorphism in the ESR2 gene (rs4986938, previously associated with endome... DisGeNET Detail
However, an interactive association with BMI was observed in the relationship between prostate cance... DisGeNET Detail
However, an interactive association with BMI was observed in the relationship between prostate cance... DisGeNET Detail
Also, the ESR2 rs4986938 (38 bp 3' of STP) GG genotype was associated with a higher risk of bile duc... DisGeNET Detail
In men, only the ER-β rs4986938 polymorphism showed a weak association with depression risk. DisGeNET Detail
To investigate whether a polymorphism in the ESR2 gene (rs4986938, previously associated with endome... DisGeNET Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs4986938 dbSNP
Genome
hg38
Position
chr14:64,233,098-64,233,098
Variant Type
snv
Reference Allele
C
Alternative Allele
T
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs4986938
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1489
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
2496
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8604
East Asian Allele Counts (ExAC)
952
East Asian Heterozygous Counts (ExAC)
838
East Asian Homozygous Counts (ExAC)
57
East Asian Allele Frequency (ExAC)
0.11064621106462111
Chromosome Counts in All Race (ExAC)
118252
Allele Counts in All Race (ExAC)
37515
Heterozygous Counts in All Race (ExAC)
24647
Homozygous Counts in All Race (ExAC)
6434
Allele Frequency in All Race (ExAC)
0.3172462199370835
Genome browser