chr6:152265522:G>C Detail (hg19) (ESR1)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr6:152,265,522-152,265,522 |
| hg38 | chr6:151,944,387-151,944,387 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_000125.3:c.975G>C | NP_000116.2:p.Pro325= |
| NM_001122741.1:c.975G>C | NP_001116213.1:p.Pro325= | |
| NM_001291230.1:c.975G>C | NP_001278159.1:p.Pro325= |
Summary
MGeND
| Clinical significance |
Benign
not provided
|
| Variant entry | 4,331 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.495 |
| ToMMo:0.494 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.510 |
Prediction
ClinVar
| Clinical Significance | |
| Review star | [No Data.] |
| Show details | |
Disease area statistics
MGeND
| Clinical significance | Last evaluated | Condition | Origin | Submission ID | Submitter | Institute | Citation | Comment | Image |
|---|---|---|---|---|---|---|---|---|---|
|
Benign
|
Centenarian |
germline
|
MGS000068
(TMGS000140) |
Kenjiro Kosaki | Keio University | ||||
|
not provided
|
cervical part of oesophagus |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
abdominal part of oesophagus |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
upper third of oesophagus |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
middle third of oesophagus |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
lower third of oesophagus |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
oesophagus, unspecified |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
fundus of stomach |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
body of stomach |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
pyloric antrum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
stomach, unspecified |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
duodenum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
jejunum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
ileum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
small intestine, unspecified |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
caecum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
appendix |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
ascending colon |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
transverse colon |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
descending colon |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
sigmoid colon |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
colon, unspecified |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
malignant neoplasm of rectosigmoid junction |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
malignant neoplasm of rectum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
anal canal |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
liver cell carcinoma |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
intrahepatic bile duct carcinoma |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
malignant neoplasm of gallbladder |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
extrahepatic bile duct |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
ampulla of vater |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
head of pancreas |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
body of pancreas |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
tail of pancreas |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
ill-defined sites within the digestive system |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
bronchus or lung, unspecified |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
retroperitoneum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan |
ClinVar
[No Data.]
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| <0.001 | Tension Headache | We aimed to explore the single-locus, haplotype and epistasis patterns and the c... | BeFree | 19673915 | Detail |
| <0.001 | Tension Headache | We aimed to explore the single-locus, haplotype and epistasis patterns and the c... | BeFree | 19673915 | Detail |
| 0.240 | Malignant neoplasm of breast | When stratified by ER status, ESR1 rs1801132, rs2046210, and rs3020314 showed st... | BeFree | 25228414 | Detail |
| 0.005 | Sporadic Breast Carcinoma | The estrogen receptor alpha C975G variant in familial and sporadic breast cancer... | BeFree | 16886637 | Detail |
| 0.003 | dementia | Significant association was found between ESR1 polymorphisms (rs9340799 [ESR1+35... | BeFree | 23567436 | Detail |
| <0.001 | Mild dementia | Significant association was found between ESR1 polymorphisms (rs9340799 [ESR1+35... | BeFree | 23567436 | Detail |
| 0.080 | breast carcinoma | When stratified by ER status, ESR1 rs1801132, rs2046210, and rs3020314 showed st... | BeFree | 25228414 | 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 |
| <0.001 | Mild dementia | Significant association was found between ESR1 polymorphisms (rs9340799 [ESR1+35... | BeFree | 23567436 | Detail |
| 0.007 | Metabolic syndrome X | To investigate genetic single nucleotide polymorphisms (SNPs) in estrogen recept... | BeFree | 22011627 | Detail |
| 0.012 | dementia | Significant association was found between ESR1 polymorphisms (rs9340799 [ESR1+35... | BeFree | 23567436 | Detail |
| 0.002 | Presenile dementia | Significant association was found between ESR1 polymorphisms (rs9340799 [ESR1+35... | BeFree | 23567436 | Detail |
| <0.001 | HIV Infections | To investigate genetic single nucleotide polymorphisms (SNPs) in estrogen recept... | BeFree | 22011627 | Detail |
| 0.003 | Presenile dementia | Significant association was found between ESR1 polymorphisms (rs9340799 [ESR1+35... | BeFree | 23567436 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| We aimed to explore the single-locus, haplotype and epistasis patterns and the contribution of oestr... | DisGeNET | Detail |
| We aimed to explore the single-locus, haplotype and epistasis patterns and the contribution of oestr... | DisGeNET | Detail |
| When stratified by ER status, ESR1 rs1801132, rs2046210, and rs3020314 showed stronger associations ... | DisGeNET | Detail |
| The estrogen receptor alpha C975G variant in familial and sporadic breast cancer: a case-control stu... | DisGeNET | Detail |
| Significant association was found between ESR1 polymorphisms (rs9340799 [ESR1+351], rs1801132 [ESR1+... | DisGeNET | Detail |
| Significant association was found between ESR1 polymorphisms (rs9340799 [ESR1+351], rs1801132 [ESR1+... | DisGeNET | Detail |
| When stratified by ER status, ESR1 rs1801132, rs2046210, and rs3020314 showed stronger associations ... | 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 |
| Significant association was found between ESR1 polymorphisms (rs9340799 [ESR1+351], rs1801132 [ESR1+... | DisGeNET | Detail |
| To investigate genetic single nucleotide polymorphisms (SNPs) in estrogen receptor-α (ERα) (ESR1, rs... | DisGeNET | Detail |
| Significant association was found between ESR1 polymorphisms (rs9340799 [ESR1+351], rs1801132 [ESR1+... | DisGeNET | Detail |
| Significant association was found between ESR1 polymorphisms (rs9340799 [ESR1+351], rs1801132 [ESR1+... | DisGeNET | Detail |
| To investigate genetic single nucleotide polymorphisms (SNPs) in estrogen receptor-α (ERα) (ESR1, rs... | DisGeNET | Detail |
| Significant association was found between ESR1 polymorphisms (rs9340799 [ESR1+351], rs1801132 [ESR1+... | 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
- -
- Genome
- hg19
- Position
- chr6:152,265,522-152,265,522
- Variant Type
- snv
- Reference Allele
- G
- Alternative Allele
- C
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1180
- Mean of sample read depth (HGVD)
- 98.40
- Standard deviation of sample read depth (HGVD)
- 45.90
- Number of reference allele (HGVD)
- 1190
- Number of alternative allele (HGVD)
- 1167
- Allele Frequency (HGVD)
- 0.49512091641917694
- Gene Symbol (HGVD)
- ESR1
- 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))
- rs1801132
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.4943
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 8285
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8618
- East Asian Allele Counts (ExAC)
- 4396
- East Asian Heterozygous Counts (ExAC)
- 2150
- East Asian Homozygous Counts (ExAC)
- 1123
- East Asian Allele Frequency (ExAC)
- 0.5100951496867022
- Chromosome Counts in All Race (ExAC)
- 121356
- Allele Counts in All Race (ExAC)
- 89342
- Heterozygous Counts in All Race (ExAC)
- 22072
- Homozygous Counts in All Race (ExAC)
- 33635
- Allele Frequency in All Race (ExAC)
- 0.7361976334091433
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