chr14:64724051:C>T Detail (hg19) (ESR2)

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Summary
Information
Links
Disease area statistics
MGeND
ClinVar
CIViC
DisGeNET
Annotation
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Information

Genome

Assembly	Position
hg19	chr14:64,724,051-64,724,051
hg38	chr14:64,257,333-64,257,333 View the variant detail on this assembly version.

HGVS

ESR2

Type	Transcript	Protein
RefSeq	NM_001271876.1:c.984G>A	NP_001258805.1:p.Val328=
	NM_001040275.1:c.984G>A	NP_001035365.1:p.Val328=
	NM_001437.2:c.984G>A	NP_001428.1:p.Val328=
	NM_001291712.1:c.984G>A	NP_001278641.1:p.Val328=
	NM_001214902.1:c.984G>A	NP_001201831.1:p.Val328=
	NM_001291723.1:c.984G>A	NP_001278652.1:p.Val328=
	NM_001271877.1:c.952+3116G>A
Ensemble	ENST00000556275.5:c.984G>A	ENST00000556275.5:p.Val328=
	ENST00000553796.5:c.984G>A	ENST00000553796.5:p.Val328=
	ENST00000353772.7:c.984G>A	ENST00000353772.7:p.Val328=
	ENST00000341099.6:c.984G>A	ENST00000341099.6:p.Val328=
	ENST00000554572.5:c.984G>A	ENST00000554572.5:p.Val328=
	ENST00000555278.5:c.984G>A	ENST00000555278.5:p.Val328=
	ENST00000557772.5:c.984G>A	ENST00000557772.5:p.Val328=
	ENST00000358599.9:c.984G>A	ENST00000358599.9:p.Val328=
	ENST00000267525.10:c.952+3116G>A

Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics	Show details

Frequency

JP	HGVD:0.292
	ToMMo:0.288
	NCBN:[No Data.]
	NCBN(Hondo):[No Data.]
	NCBN(Ryukyu):[No Data.]
East asia	ExAC:0.370

Prediction

ClinVar

Clinical Significance	Benign
Review star
Show details

Links

ESR2

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	tgv51069409	TogoVar
	COSMIC
	MONDO

Disease area statistics

[No Data.]

MGeND

[No Data.]

ClinVar

Clinical significance	Last evaluated	Review status	Condition	Origin	Links
Benign	2024-01-29	criteria provided, multiple submitters, no conflicts	not provided	germline	Detail
Benign	2019-02-22	criteria provided, single submitter	ESR2-related disorder	germline	Detail

CIViC

[No Data.]

DisGeNET

Score	Disease name	Description	Source	Pubmed	Links
0.006	Degenerative polyarthritis	To investigate the possible influence of the single nucleotide polymorphism (SNP...	BeFree	21523342	Detail
0.030	breast carcinoma	The ESR2 rs4986938 and rs1256049 polymorphisms were described to present associa...	BeFree	25341980	Detail
0.009	atherosclerosis	In a Finnish population, the ESR2 rs1256049 polymorphism A allele is associated ...	BeFree	18939943	Detail
0.006	Degenerative polyarthritis	The rs1256049 polymorphism of the estrogen receptor-β gene can potentially be us...	BeFree	23352710	Detail
<0.001	Phobic anxiety disorder	The A allele of ESR2 rs1256049 was associated with an increased risk of GAD [OR:...	BeFree	21570196	Detail
0.068	Malignant neoplasm of breast	The ESR2 rs4986938 and rs1256049 polymorphisms were described to present associa...	BeFree	25341980	Detail
0.024	prostate carcinoma	The influence of ESR1 rs9340799 and ESR2 rs1256049 polymorphisms on prostate can...	BeFree	24859835	Detail
0.087	obesity	The relationship of three polymorphisms (rs1271572, rs1256049 and rs4986938) and...	BeFree	19111408	Detail
0.061	Malignant neoplasm of prostate	The influence of ESR1 rs9340799 and ESR2 rs1256049 polymorphisms on prostate can...	BeFree	24859835	Detail
0.044	Malignant neoplasm of prostate	The influence of ESR1 rs9340799 and ESR2 rs1256049 polymorphisms on prostate can...	BeFree	24859835	Detail
0.011	prostate carcinoma	The influence of ESR1 rs9340799 and ESR2 rs1256049 polymorphisms on prostate can...	BeFree	24859835	Detail
0.001	arteriosclerosis	In a Finnish population, the ESR2 rs1256049 polymorphism A allele is associated ...	BeFree	18939943	Detail
0.008	male infertility	[The RsaI polymorphism in the estrogen receptor-beta gene is associated with mal...	GAD	15998774	Detail

Annotation

Annotations

Descrption	Source	Links
NM_001437.3(ESR2):c.984G>A (p.Val328=) AND not provided	ClinVar	Detail
NM_001437.3(ESR2):c.984G>A (p.Val328=) AND ESR2-related disorder	ClinVar	Detail
To investigate the possible influence of the single nucleotide polymorphism (SNP) of the estrogen re...	DisGeNET	Detail
The ESR2 rs4986938 and rs1256049 polymorphisms were described to present association with breast can...	DisGeNET	Detail
In a Finnish population, the ESR2 rs1256049 polymorphism A allele is associated with preclinical ath...	DisGeNET	Detail
The rs1256049 polymorphism of the estrogen receptor-β gene can potentially be used to identify genet...	DisGeNET	Detail
The A allele of ESR2 rs1256049 was associated with an increased risk of GAD [OR: 2.06, 95% CI: 1.09-...	DisGeNET	Detail
The ESR2 rs4986938 and rs1256049 polymorphisms were described to present association with breast can...	DisGeNET	Detail
The influence of ESR1 rs9340799 and ESR2 rs1256049 polymorphisms on prostate cancer risk.	DisGeNET	Detail
The relationship of three polymorphisms (rs1271572, rs1256049 and rs4986938) and their associated ha...	DisGeNET	Detail
The influence of ESR1 rs9340799 and ESR2 rs1256049 polymorphisms on prostate cancer risk.	DisGeNET	Detail
The influence of ESR1 rs9340799 and ESR2 rs1256049 polymorphisms on prostate cancer risk.	DisGeNET	Detail
The influence of ESR1 rs9340799 and ESR2 rs1256049 polymorphisms on prostate cancer risk.	DisGeNET	Detail
In a Finnish population, the ESR2 rs1256049 polymorphism A allele is associated with preclinical ath...	DisGeNET	Detail
[The RsaI polymorphism in the estrogen receptor-beta gene is associated with male infertility.]	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: rs1256049 dbSNP
Genome: hg19
Position: chr14:64,724,051-64,724,051
Variant Type: snv
Reference Allele: C
Alternative Allele: T
Filtering Status (HGVD): PASS
# of samples (HGVD): 1208
Mean of sample read depth (HGVD): 45.18
Standard deviation of sample read depth (HGVD): 27.36
Number of reference allele (HGVD): 1711
Number of alternative allele (HGVD): 705
Allele Frequency (HGVD): 0.2918046357615894
Gene Symbol (HGVD): ESR2
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)): rs1256049
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 0.2884
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 4834
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 16760
East Asian Chromosome Counts (ExAC): 8638
East Asian Allele Counts (ExAC): 3193
East Asian Heterozygous Counts (ExAC): 1995
East Asian Homozygous Counts (ExAC): 599
East Asian Allele Frequency (ExAC): 0.3696457513313267
Chromosome Counts in All Race (ExAC): 121340
Allele Counts in All Race (ExAC): 8138
Heterozygous Counts in All Race (ExAC): 6644
Homozygous Counts in All Race (ExAC): 747
Allele Frequency in All Race (ExAC): 0.06706774353057525

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