chr17:41244000:T>C Detail (hg19) (BRCA1, LOC126862571)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr17:41,244,000-41,244,000 |
| hg38 | chr17:43,091,983-43,091,983 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_007297.3:c.3407A>G | NP_009228.2:p.Lys1136Arg |
| NM_007299.3:c.788-951A>G | ||
| NM_007298.3:c.788-951A>G |
Summary
MGeND
| Clinical significance |
Benign
Likely benign
Uncertain significance
|
| Variant entry | 5,087 |
| GWAS entry | |
| Disease area statistics | Show details |
Frequency
| JP | HGVD:0.330 |
| ToMMo:0.328 | |
| NCBN:[No Data.] | |
| NCBN(Hondo):[No Data.] | |
| NCBN(Ryukyu):[No Data.] | |
| East asia | ExAC:0.383 |
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 |
|---|---|---|---|---|---|---|---|---|---|
|
Likely benign
|
2020/04/20 | colon, unspecified |
not provided
|
MGS000040
(TMGS000095) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Benign
|
2018/01/13 | breast, unspecified |
germline
|
MGS000028
(TMGS000049) |
Yukihide Momozawa | RIKEN |
30287823
|
||
|
Uncertain significance
|
Others |
somatic
|
MGS000038
(TMGS000091) |
Manabu Muto Ichiro Kinoshita |
Kyoto University Department of Medical Oncology Faculty of Medicine and Graduate School of Medicine Hokkaido University |
||||
|
Benign
|
Centenarian |
germline
|
MGS000068
(TMGS000140) |
Kenjiro Kosaki | Keio University | ||||
|
Likely benign
|
2020/04/20 | cervical part of oesophagus |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | upper third of oesophagus |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | middle third of oesophagus |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | lower third of oesophagus |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | oesophagus, unspecified |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | fundus of stomach |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | body of stomach |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | pyloric antrum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | stomach, unspecified |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | duodenum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | jejunum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | small intestine, unspecified |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | caecum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | appendix |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | ascending colon |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | transverse colon |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | descending colon |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | sigmoid colon |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | colon, unspecified |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | malignant neoplasm of rectosigmoid junction |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | malignant neoplasm of rectum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | anal canal |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | liver cell carcinoma |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | intrahepatic bile duct carcinoma |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | malignant neoplasm of gallbladder |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | extrahepatic bile duct |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | ampulla of vater |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | head of pancreas |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | body of pancreas |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | tail of pancreas |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | ill-defined sites within the digestive system |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | bronchus or lung, unspecified |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | other |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | cervical part of oesophagus |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | abdominal part of oesophagus |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | upper third of oesophagus |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | middle third of oesophagus |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | lower third of oesophagus |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | oesophagus, unspecified |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | fundus of stomach |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | body of stomach |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | pyloric antrum |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | stomach, unspecified |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | duodenum |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | jejunum |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | ileum |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | small intestine, unspecified |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | caecum |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | appendix |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | transverse colon |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | descending colon |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | overlapping lesion of colon |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | colon, unspecified |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | malignant neoplasm of rectosigmoid junction |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | malignant neoplasm of rectum |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | anal canal |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | liver cell carcinoma |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | intrahepatic bile duct carcinoma |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | malignant neoplasm of gallbladder |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | extrahepatic bile duct |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | ampulla of vater |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | head of pancreas |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | body of pancreas |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | tail of pancreas |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | ill-defined sites within the digestive system |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan | |||
|
Likely benign
|
2020/04/20 | bronchus or lung, unspecified |
not provided
|
MGS000041
(TMGS000094) |
Hitoshi Nakagama | National Cancer Center Japan |
ClinVar
| Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
|---|---|---|---|---|---|
|
Benign
|
2023-11-29 | criteria provided, single submitter | not provided |
unknown
germline
|
Detail |
|
Benign
|
2024-02-01 | criteria provided, multiple submitters, no conflicts | hereditary breast ovarian cancer syndrome |
germline
|
Detail |
|
Benign
|
2015-08-10 | reviewed by expert panel | Breast-ovarian cancer, familial, susceptibility to, 1 |
germline
not provided
unknown
|
Detail |
|
Benign
|
2017-11-01 | criteria provided, multiple submitters, no conflicts | not specified |
germline
unknown
|
Detail |
|
Benign
|
2019-12-11 | criteria provided, multiple submitters, no conflicts | Hereditary cancer-predisposing syndrome |
germline
|
Detail |
|
Benign
|
2020-05-03 | criteria provided, multiple submitters, no conflicts | Familial cancer of breast |
germline
unknown
|
Detail |
|
Benign
|
2019-04-22 | criteria provided, single submitter | breast carcinoma |
germline
|
Detail |
|
Benign
|
2022-05-06 | criteria provided, single submitter | Familial cancer of breast,Pancreatic cancer, susceptibility to, 4,Fanconi anemia, complementation group S,Breast-ovarian cancer, familial, susceptibility to, 1 |
unknown
|
Detail |
|
Benign
|
2022-05-06 | criteria provided, single submitter | Familial cancer of breast,Pancreatic cancer, susceptibility to, 4,Fanconi anemia, complementation group S,Breast-ovarian cancer, familial, susceptibility to, 1 |
unknown
|
Detail |
|
Benign
|
2022-05-06 | criteria provided, single submitter | Familial cancer of breast,Pancreatic cancer, susceptibility to, 4,Fanconi anemia, complementation group S,Breast-ovarian cancer, familial, susceptibility to, 1 |
unknown
|
Detail |
|
Benign
|
2022-05-06 | criteria provided, single submitter | Familial cancer of breast,Pancreatic cancer, susceptibility to, 4,Fanconi anemia, complementation group S,Breast-ovarian cancer, familial, susceptibility to, 1 |
unknown
|
Detail |
CIViC
[No Data.]
DisGeNET
| Score | Disease name | Description | Source | Pubmed | Links |
|---|---|---|---|---|---|
| 0.080 | breast carcinoma | Polymorphic coding and noncoding variants were transmitted in each family's rela... | BeFree | 20352487 | Detail |
| 0.480 | Malignant neoplasm of breast | Polymorphic coding and noncoding variants were transmitted in each family's rela... | BeFree | 20352487 | Detail |
| 0.360 | Malignant neoplasm of breast | Polymorphic coding and noncoding variants were transmitted in each family's rela... | BeFree | 20352487 | Detail |
| 0.080 | breast carcinoma | Polymorphic coding and noncoding variants were transmitted in each family's rela... | BeFree | 20352487 | Detail |
| 0.196 | Breast Cancer, Familial | Association of BRCA1 K1183R polymorphism with survival in BRCA1/2-negative chine... | BeFree | 24600974 | Detail |
| <0.001 | Small cell carcinoma of esophagus | We retrospectively examined whether there was an association between the selecte... | BeFree | 25374063 | Detail |
| <0.001 | Small cell carcinoma of esophagus | We retrospectively examined whether there was an association between the selecte... | BeFree | 25374063 | Detail |
| <0.001 | Small cell carcinoma of esophagus | We retrospectively examined whether there was an association between the selecte... | BeFree | 25374063 | Detail |
| <0.001 | Small cell carcinoma of esophagus | We retrospectively examined whether there was an association between the selecte... | BeFree | 25374063 | Detail |
| <0.001 | Small cell carcinoma of esophagus | We retrospectively examined whether there was an association between the selecte... | BeFree | 25374063 | Detail |
Annotation
Annotations
| Descrption | Source | Links |
|---|---|---|
| NM_007294.4(BRCA1):c.3548A>G (p.Lys1183Arg) AND not provided | ClinVar | Detail |
| NM_007294.4(BRCA1):c.3548A>G (p.Lys1183Arg) AND Hereditary breast ovarian cancer syndrome | ClinVar | Detail |
| NM_007294.4(BRCA1):c.3548A>G (p.Lys1183Arg) AND Breast-ovarian cancer, familial, susceptibility to, ... | ClinVar | Detail |
| NM_007294.4(BRCA1):c.3548A>G (p.Lys1183Arg) AND not specified | ClinVar | Detail |
| NM_007294.4(BRCA1):c.3548A>G (p.Lys1183Arg) AND Hereditary cancer-predisposing syndrome | ClinVar | Detail |
| NM_007294.4(BRCA1):c.3548A>G (p.Lys1183Arg) AND Familial cancer of breast | ClinVar | Detail |
| NM_007294.4(BRCA1):c.3548A>G (p.Lys1183Arg) AND Breast carcinoma | ClinVar | Detail |
| NM_007294.4(BRCA1):c.3548A>G (p.Lys1183Arg) AND multiple conditions | ClinVar | Detail |
| NM_007294.4(BRCA1):c.3548A>G (p.Lys1183Arg) AND multiple conditions | ClinVar | Detail |
| NM_007294.4(BRCA1):c.3548A>G (p.Lys1183Arg) AND multiple conditions | ClinVar | Detail |
| NM_007294.4(BRCA1):c.3548A>G (p.Lys1183Arg) AND multiple conditions | ClinVar | Detail |
| Polymorphic coding and noncoding variants were transmitted in each family's relatives with a frequen... | DisGeNET | Detail |
| Polymorphic coding and noncoding variants were transmitted in each family's relatives with a frequen... | DisGeNET | Detail |
| Polymorphic coding and noncoding variants were transmitted in each family's relatives with a frequen... | DisGeNET | Detail |
| Polymorphic coding and noncoding variants were transmitted in each family's relatives with a frequen... | DisGeNET | Detail |
| Association of BRCA1 K1183R polymorphism with survival in BRCA1/2-negative chinese familial breast c... | DisGeNET | Detail |
| We retrospectively examined whether there was an association between the selected six single nucleot... | DisGeNET | Detail |
| We retrospectively examined whether there was an association between the selected six single nucleot... | DisGeNET | Detail |
| We retrospectively examined whether there was an association between the selected six single nucleot... | DisGeNET | Detail |
| We retrospectively examined whether there was an association between the selected six single nucleot... | DisGeNET | Detail |
| We retrospectively examined whether there was an association between the selected six single nucleot... | 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
- rs16942 dbSNP
- Genome
- hg19
- Position
- chr17:41,244,000-41,244,000
- Variant Type
- snv
- Reference Allele
- T
- Alternative Allele
- C
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1210
- Mean of sample read depth (HGVD)
- 126.28
- Standard deviation of sample read depth (HGVD)
- 57.03
- Number of reference allele (HGVD)
- 1621
- Number of alternative allele (HGVD)
- 797
- Allele Frequency (HGVD)
- 0.3296112489660877
- Gene Symbol (HGVD)
- BRCA1
- 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))
- rs16942
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.3277
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 5492
- Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 16760
- East Asian Chromosome Counts (ExAC)
- 8508
- East Asian Allele Counts (ExAC)
- 3256
- East Asian Heterozygous Counts (ExAC)
- 1992
- East Asian Homozygous Counts (ExAC)
- 632
- East Asian Allele Frequency (ExAC)
- 0.382698636577339
- Chromosome Counts in All Race (ExAC)
- 120772
- Allele Counts in All Race (ExAC)
- 42150
- Heterozygous Counts in All Race (ExAC)
- 26614
- Homozygous Counts in All Race (ExAC)
- 7768
- Allele Frequency in All Race (ExAC)
- 0.3490047361971318
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