chr17:43091983:T>C Detail (hg38) (BRCA1, LOC126862571)
Information
Genome
Assembly | Position |
---|---|
hg19 | chr17:41,244,000-41,244,000 View the variant detail on this assembly version. |
hg38 | chr17:43,091,983-43,091,983 |
HGVS
Type | Transcript | Protein |
---|---|---|
RefSeq | NM_007294.3:c.3548A>G | NP_009225.1:p.Lys1183Arg |
NM_007299.3:c.788-951A>G | ||
NM_007300.3:c.3548A>G | NP_009231.2:p.Lys1183Arg |
Summary
MGeND
Clinical significance |
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Variant entry | 1 |
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 |
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Review star | ![]() |
Show details |
Disease area statistics
MGeND
Clinical significance | Last evaluated | Condition | Origin | Submission ID | Submitter | Institute | Citation | Comment | Image |
---|---|---|---|---|---|---|---|---|---|
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Centenarian |
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MGS000068
(TMGS000140) |
Kenjiro Kosaki | Keio University |
ClinVar
Clinical significance | Last evaluated | Review status | Condition | Origin | Links |
---|---|---|---|---|---|
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2023-11-29 | criteria provided, single submitter | not provided |
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Detail |
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2024-02-01 | criteria provided, multiple submitters, no conflicts | hereditary breast ovarian cancer syndrome |
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Detail |
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2015-08-10 | reviewed by expert panel | Breast-ovarian cancer, familial, susceptibility to, 1 |
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Detail |
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2017-11-01 | criteria provided, multiple submitters, no conflicts | not specified |
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Detail |
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2019-12-11 | criteria provided, multiple submitters, no conflicts | Hereditary cancer-predisposing syndrome |
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Detail |
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2020-05-03 | criteria provided, multiple submitters, no conflicts | Familial cancer of breast |
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Detail |
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2019-04-22 | criteria provided, single submitter | breast carcinoma |
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Detail |
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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 |
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Detail |
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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 |
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Detail |
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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 |
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Detail |
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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 |
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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 |
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Overlapped Transcript
Gene | Transcript ID | Chromosome | Start | Stop | Links |
---|
- Gene
- -
- dbSNP
- rs16942 dbSNP
- Genome
- hg38
- Position
- chr17:43,091,983-43,091,983
- 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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