chr6:152129077:T>C Detail (hg19) (ESR1)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr6:152,129,077-152,129,077 |
| hg38 | chr6:151,807,942-151,807,942 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_000125.3:c.30T>C | NP_000116.2:p.Ser10= |
| NM_001122741.1:c.30T>C | NP_001116213.1:p.Ser10= | |
| NM_001291230.1:c.30T>C | NP_001278159.1:p.Ser10= |
Summary
MGeND
| Clinical significance |
not provided
|
| Variant entry | 3,680 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.401 |
| ToMMo:0.401 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.363 |
Prediction
ClinVar
| Clinical Significance |
Benign
|
| Review star |  |
| Show details | |
Disease area statistics
MGeND
| Clinical significance | Last evaluated | Condition | Origin | Submission ID | Submitter | Institute | Citation | Comment | Image |
|---|---|---|---|---|---|---|---|---|---|
|
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 | ||||
|
not provided
|
other |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Benign
|
2018-08-17 | criteria provided, single submitter | not provided |
germline
|
Detail |
|
Benign
|
2022-04-19 | criteria provided, single submitter | Familial cancer of breast,Myocardial infarction, susceptibility to,Migraine with or without aura, susceptibility to, 1,Estrogen resistance syndrome |
unknown
|
Detail |
|
Benign
|
2022-04-19 | criteria provided, single submitter | Familial cancer of breast,Myocardial infarction, susceptibility to,Migraine with or without aura, susceptibility to, 1,Estrogen resistance syndrome |
unknown
|
Detail |
|
Benign
|
2022-04-19 | criteria provided, single submitter | Familial cancer of breast,Myocardial infarction, susceptibility to,Migraine with or without aura, susceptibility to, 1,Estrogen resistance syndrome |
unknown
|
Detail |
|
Benign
|
2022-04-19 | criteria provided, single submitter | Familial cancer of breast,Myocardial infarction, susceptibility to,Migraine with or without aura, susceptibility to, 1,Estrogen resistance syndrome |
unknown
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.007 | prostate carcinoma | The combination of the TTTA long repeats and the minor alleles of rs10046 in CYP... | BeFree | 19952760 | Detail |
| 0.061 | Malignant neoplasm of prostate | The combination of the TTTA long repeats and the minor alleles of rs10046 in CYP... | BeFree | 19952760 | Detail |
| 0.024 | prostate carcinoma | The combination of the TTTA long repeats and the minor alleles of rs10046 in CYP... | BeFree | 19952760 | Detail |
| 0.051 | Malignant neoplasm of prostate | The combination of the TTTA long repeats and the minor alleles of rs10046 in CYP... | BeFree | 19952760 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_000125.4(ESR1):c.30T>C (p.Ser10=) AND not provided | ClinVar | Detail |
| NM_000125.4(ESR1):c.30T>C (p.Ser10=) AND multiple conditions | ClinVar | Detail |
| NM_000125.4(ESR1):c.30T>C (p.Ser10=) AND multiple conditions | ClinVar | Detail |
| NM_000125.4(ESR1):c.30T>C (p.Ser10=) AND multiple conditions | ClinVar | Detail |
| NM_000125.4(ESR1):c.30T>C (p.Ser10=) AND multiple conditions | ClinVar | Detail |
| The combination of the TTTA long repeats and the minor alleles of rs10046 in CYP19A1 and rs2077647 i... | DisGeNET | Detail |
| The combination of the TTTA long repeats and the minor alleles of rs10046 in CYP19A1 and rs2077647 i... | DisGeNET | Detail |
| The combination of the TTTA long repeats and the minor alleles of rs10046 in CYP19A1 and rs2077647 i... | DisGeNET | Detail |
| The combination of the TTTA long repeats and the minor alleles of rs10046 in CYP19A1 and rs2077647 i... | 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
- rs2077647 dbSNP
- Genome
- hg19
- Position
- chr6:152,129,077-152,129,077
- Variant Type
- snv
- Reference Allele
- T
- Alternative Allele
- C
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1210
- Mean of sample read depth (HGVD)
- 220.06
- Standard deviation of sample read depth (HGVD)
- 99.17
- Number of reference allele (HGVD)
- 1450
- Number of alternative allele (HGVD)
- 970
- Allele Frequency (HGVD)
- 0.40082644628099173
- 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))
- rs2077647
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.4013
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 6726
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8538
- East Asian Allele Counts (ExAC)
- 3102
- East Asian Heterozygous Counts (ExAC)
- 2004
- East Asian Homozygous Counts (ExAC)
- 549
- East Asian Allele Frequency (ExAC)
- 0.36331693605059734
- Chromosome Counts in All Race (ExAC)
- 119490
- Allele Counts in All Race (ExAC)
- 55608
- Heterozygous Counts in All Race (ExAC)
- 29735
- Homozygous Counts in All Race (ExAC)
- 12936
- Allele Frequency in All Race (ExAC)
- 0.46537785588752195
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