chr3:142281612:A>G Detail (hg19) (ATR)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr3:142,281,612-142,281,612 |
| hg38 | chr3:142,562,770-142,562,770 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_001184.3:c.632T>C | NP_001175.2:p.Met211Thr |
| Ensemble | ENST00000350721.9:c.632T>C | ENST00000350721.9:p.Met211Thr |
| ENST00000661310.1:c.632T>C | ENST00000661310.1:p.Met211Thr |
Summary
MGeND
| Clinical significance |
Benign
|
| Variant entry | 3,836 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.421 |
| ToMMo:0.434 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.466 |
Prediction
ClinVar
| Clinical Significance |
Benign
Likely benign
|
| Review star |  |
| Show details | |
Disease area statistics
MGeND
| Clinical significance | Last evaluated | Condition | Origin | Submission ID | Submitter | Institute | Citation | Comment | Image |
|---|---|---|---|---|---|---|---|---|---|
|
Benign
|
2020/04/20 | cervical part of oesophagus |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | abdominal part of oesophagus |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | upper third of oesophagus |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | middle third of oesophagus |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | lower third of oesophagus |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | oesophagus, unspecified |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | fundus of stomach |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | body of stomach |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | pyloric antrum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | stomach, unspecified |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | duodenum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | jejunum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | ileum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | small intestine, unspecified |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | caecum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | appendix |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | ascending colon |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | transverse colon |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | descending colon |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | sigmoid colon |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | colon, unspecified |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | malignant neoplasm of rectosigmoid junction |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | malignant neoplasm of rectum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | anal canal |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | liver cell carcinoma |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | intrahepatic bile duct carcinoma |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | malignant neoplasm of gallbladder |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | extrahepatic bile duct |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | ampulla of vater |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | head of pancreas |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | body of pancreas |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | tail of pancreas |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | ill-defined sites within the digestive system |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | bronchus or lung, unspecified |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2020/04/20 | other |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Benign
Likely benign
|
2016-03-28 | criteria provided, multiple submitters, no conflicts | not specified |
germline
|
Detail |
|
Benign
|
2021-07-14 | criteria provided, multiple submitters, no conflicts | Seckel syndrome 1 |
germline
|
Detail |
|
Benign
|
2024-02-01 | criteria provided, multiple submitters, no conflicts | not provided |
germline
|
Detail |
|
Benign
|
2023-07-07 | criteria provided, single submitter | Familial cutaneous telangiectasia and oropharyngeal predisposition cancer syndrome |
germline
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.002 | Non-small cell lung carcinoma | Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8... | BeFree | 16195237 | Detail |
| 0.156 | Non-small cell lung carcinoma | Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8... | BeFree | 16195237 | Detail |
| 0.005 | Non-small cell lung carcinoma | Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8... | BeFree | 16195237 | Detail |
| 0.004 | Non-small cell lung carcinoma | Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8... | BeFree | 16195237 | Detail |
| <0.001 | Non-small cell lung carcinoma | Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8... | BeFree | 16195237 | Detail |
| <0.001 | Non-small cell lung carcinoma | Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8... | BeFree | 16195237 | Detail |
| 0.002 | Non-small cell lung carcinoma | Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8... | BeFree | 16195237 | Detail |
| <0.001 | Non-small cell lung carcinoma | Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8... | BeFree | 16195237 | Detail |
| 0.001 | Non-small cell lung carcinoma | Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8... | BeFree | 16195237 | Detail |
| 0.012 | Non-small cell lung carcinoma | Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8... | BeFree | 16195237 | Detail |
| 0.004 | Non-small cell lung carcinoma | Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8... | BeFree | 16195237 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_001184.4(ATR):c.632T>C (p.Met211Thr) AND not specified | ClinVar | Detail |
| NM_001184.4(ATR):c.632T>C (p.Met211Thr) AND Seckel syndrome 1 | ClinVar | Detail |
| NM_001184.4(ATR):c.632T>C (p.Met211Thr) AND not provided | ClinVar | Detail |
| NM_001184.4(ATR):c.632T>C (p.Met211Thr) AND Familial cutaneous telangiectasia and oropharyngeal pred... | ClinVar | Detail |
| Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8902G>T), XPA (-4G... | DisGeNET | Detail |
| Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8902G>T), XPA (-4G... | DisGeNET | Detail |
| Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8902G>T), XPA (-4G... | DisGeNET | Detail |
| Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8902G>T), XPA (-4G... | DisGeNET | Detail |
| Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8902G>T), XPA (-4G... | DisGeNET | Detail |
| Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8902G>T), XPA (-4G... | DisGeNET | Detail |
| Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8902G>T), XPA (-4G... | DisGeNET | Detail |
| Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8902G>T), XPA (-4G... | DisGeNET | Detail |
| Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8902G>T), XPA (-4G... | DisGeNET | Detail |
| Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8902G>T), XPA (-4G... | DisGeNET | Detail |
| Our results indicate that SNPs in the NER genes ERCC1 (Asn118Asn, 15310G>C, 8902G>T), XPA (-4G... | 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
- rs2227928 dbSNP
- Genome
- hg19
- Position
- chr3:142,281,612-142,281,612
- Variant Type
- snv
- Reference Allele
- A
- Alternative Allele
- G
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1210
- Mean of sample read depth (HGVD)
- 80.48
- Standard deviation of sample read depth (HGVD)
- 33.22
- Number of reference allele (HGVD)
- 1401
- Number of alternative allele (HGVD)
- 1019
- Allele Frequency (HGVD)
- 0.42107438016528925
- Gene Symbol (HGVD)
- ATR
- East Asian Homozygous Counts (ExAC)
- 945
- 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))
- rs2227928
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.4339
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 7272
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8578
- East Asian Allele Counts (ExAC)
- 3996
- East Asian Heterozygous Counts (ExAC)
- 2106
- East Asian Allele Frequency (ExAC)
- 0.4658428538120774
- Chromosome Counts in All Race (ExAC)
- 120592
- Allele Counts in All Race (ExAC)
- 66806
- Heterozygous Counts in All Race (ExAC)
- 28610
- Homozygous Counts in All Race (ExAC)
- 19098
- Allele Frequency in All Race (ExAC)
- 0.5539836805094865
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