chr17:41223094:T>C Detail (hg19) (BRCA1)

Information

Genome

Assembly Position
hg19 chr17:41,223,094-41,223,094
hg38 chr17:43,071,077-43,071,077 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_007300.3:c.4900A>G NP_009231.2:p.Ser1634Gly
NM_007298.3:c.1525A>G NP_009229.2:p.Ser509Gly
NM_007294.3:c.4837A>G NP_009225.1:p.Ser1613Gly
Summary

MGeND

Clinical significance Benign Likely benign Uncertain significance
Variant entry 5,092
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.331
ToMMo:0.328
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.381

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 113705 OMIM
HGNC 1100 HGNC
Ensembl ENSG00000012048 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv57841033 TogoVar
COSMIC COSM3755560 COSMIC
MONDO
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 2020-05-03 criteria provided, multiple submitters, no conflicts Familial cancer of breast germline unknown Detail
Benign 2015-08-10 reviewed by expert panel Breast-ovarian cancer, familial, susceptibility to, 1 germline not provided somatic unknown Detail
Benign 2024-02-01 criteria provided, multiple submitters, no conflicts hereditary breast ovarian cancer syndrome germline Detail
Benign 2017-11-01 criteria provided, multiple submitters, no conflicts not specified germline unknown Detail
Benign 2022-01-02 criteria provided, multiple submitters, no conflicts Hereditary cancer-predisposing syndrome germline Detail
Benign 2019-04-03 criteria provided, single submitter breast carcinoma germline Detail
Benign no assertion criteria provided germline Detail
Benign 2022-05-06 criteria provided, single submitter Breast-ovarian cancer, familial, susceptibility to, 1,Fanconi anemia, complementation group S,Familial cancer of breast,Pancreatic cancer, susceptibility to, 4 unknown Detail
Benign 2022-05-06 criteria provided, single submitter Breast-ovarian cancer, familial, susceptibility to, 1,Fanconi anemia, complementation group S,Familial cancer of breast,Pancreatic cancer, susceptibility to, 4 unknown Detail
Benign 2022-05-06 criteria provided, single submitter Breast-ovarian cancer, familial, susceptibility to, 1,Fanconi anemia, complementation group S,Familial cancer of breast,Pancreatic cancer, susceptibility to, 4 unknown Detail
Benign 2022-05-06 criteria provided, single submitter Breast-ovarian cancer, familial, susceptibility to, 1,Fanconi anemia, complementation group S,Familial cancer of breast,Pancreatic cancer, susceptibility to, 4 unknown Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.042 breast carcinoma We aimed to determine the associations of genetic polymorphisms of excision repa... BeFree 24933103 Detail
0.005 Non-small cell lung carcinoma We aimed to determine the associations of genetic polymorphisms of excision repa... BeFree 24933103 Detail
0.012 Non-small cell lung carcinoma We aimed to determine the associations of genetic polymorphisms of excision repa... BeFree 24933103 Detail
0.002 Xeroderma Pigmentosum, Complementation Group D We aimed to determine the associations of genetic polymorphisms of excision repa... BeFree 24933103 Detail
0.098 Malignant neoplasm of breast We aimed to determine the associations of genetic polymorphisms of excision repa... BeFree 24933103 Detail
0.080 breast carcinoma We aimed to determine the associations of genetic polymorphisms of excision repa... BeFree 24933103 Detail
0.018 Malignant neoplasm of breast We aimed to determine the associations of genetic polymorphisms of excision repa... BeFree 24933103 Detail
0.005 Non-small cell lung carcinoma We aimed to determine the associations of genetic polymorphisms of excision repa... BeFree 24933103 Detail
0.084 Malignant neoplasm of breast We aimed to determine the associations of genetic polymorphisms of excision repa... BeFree 24933103 Detail
0.018 breast carcinoma We aimed to determine the associations of genetic polymorphisms of excision repa... BeFree 24933103 Detail
0.011 breast carcinoma We aimed to determine the associations of genetic polymorphisms of excision repa... BeFree 24933103 Detail
0.360 Malignant neoplasm of breast We aimed to determine the associations of genetic polymorphisms of excision repa... BeFree 24933103 Detail
0.097 Malignant neoplasm of breast We aimed to determine the associations of genetic polymorphisms of excision repa... BeFree 24933103 Detail
0.085 Malignant neoplasm of breast We aimed to determine the associations of genetic polymorphisms of excision repa... BeFree 24933103 Detail
0.008 breast carcinoma We aimed to determine the associations of genetic polymorphisms of excision repa... BeFree 24933103 Detail
0.006 breast carcinoma We aimed to determine the associations of genetic polymorphisms of excision repa... BeFree 24933103 Detail
0.009 Non-small cell lung carcinoma Survival analyses indicated that BRCA1 rs1799966 TC+CC genotypes were associated... BeFree 24933103 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_007294.4(BRCA1):c.4837A>G (p.Ser1613Gly) AND not provided ClinVar Detail
NM_007294.4(BRCA1):c.4837A>G (p.Ser1613Gly) AND Familial cancer of breast ClinVar Detail
NM_007294.4(BRCA1):c.4837A>G (p.Ser1613Gly) AND Breast-ovarian cancer, familial, susceptibility to, ... ClinVar Detail
NM_007294.4(BRCA1):c.4837A>G (p.Ser1613Gly) AND Hereditary breast ovarian cancer syndrome ClinVar Detail
NM_007294.4(BRCA1):c.4837A>G (p.Ser1613Gly) AND not specified ClinVar Detail
NM_007294.4(BRCA1):c.4837A>G (p.Ser1613Gly) AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_007294.4(BRCA1):c.4837A>G (p.Ser1613Gly) AND Breast carcinoma ClinVar Detail
NM_007294.4(BRCA1):c.4837A>G (p.Ser1613Gly) AND Malignant tumor of breast ClinVar Detail
NM_007294.4(BRCA1):c.4837A>G (p.Ser1613Gly) AND multiple conditions ClinVar Detail
NM_007294.4(BRCA1):c.4837A>G (p.Ser1613Gly) AND multiple conditions ClinVar Detail
NM_007294.4(BRCA1):c.4837A>G (p.Ser1613Gly) AND multiple conditions ClinVar Detail
NM_007294.4(BRCA1):c.4837A>G (p.Ser1613Gly) AND multiple conditions ClinVar Detail
We aimed to determine the associations of genetic polymorphisms of excision repair cross-complementa... DisGeNET Detail
We aimed to determine the associations of genetic polymorphisms of excision repair cross-complementa... DisGeNET Detail
We aimed to determine the associations of genetic polymorphisms of excision repair cross-complementa... DisGeNET Detail
We aimed to determine the associations of genetic polymorphisms of excision repair cross-complementa... DisGeNET Detail
We aimed to determine the associations of genetic polymorphisms of excision repair cross-complementa... DisGeNET Detail
We aimed to determine the associations of genetic polymorphisms of excision repair cross-complementa... DisGeNET Detail
We aimed to determine the associations of genetic polymorphisms of excision repair cross-complementa... DisGeNET Detail
We aimed to determine the associations of genetic polymorphisms of excision repair cross-complementa... DisGeNET Detail
We aimed to determine the associations of genetic polymorphisms of excision repair cross-complementa... DisGeNET Detail
We aimed to determine the associations of genetic polymorphisms of excision repair cross-complementa... DisGeNET Detail
We aimed to determine the associations of genetic polymorphisms of excision repair cross-complementa... DisGeNET Detail
We aimed to determine the associations of genetic polymorphisms of excision repair cross-complementa... DisGeNET Detail
We aimed to determine the associations of genetic polymorphisms of excision repair cross-complementa... DisGeNET Detail
We aimed to determine the associations of genetic polymorphisms of excision repair cross-complementa... DisGeNET Detail
We aimed to determine the associations of genetic polymorphisms of excision repair cross-complementa... DisGeNET Detail
We aimed to determine the associations of genetic polymorphisms of excision repair cross-complementa... DisGeNET Detail
Survival analyses indicated that BRCA1 rs1799966 TC+CC genotypes were associated with a decreased ri... 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
rs1799966 dbSNP
Genome
hg19
Position
chr17:41,223,094-41,223,094
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
240.46
Standard deviation of sample read depth (HGVD)
107.00
Number of reference allele (HGVD)
1620
Number of alternative allele (HGVD)
800
Allele Frequency (HGVD)
0.3305785123966942
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))
rs1799966
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.328
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
5498
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8612
East Asian Allele Counts (ExAC)
3277
East Asian Heterozygous Counts (ExAC)
1993
East Asian Homozygous Counts (ExAC)
642
East Asian Allele Frequency (ExAC)
0.3805155596841616
Chromosome Counts in All Race (ExAC)
121360
Allele Counts in All Race (ExAC)
42424
Heterozygous Counts in All Race (ExAC)
26717
Homozygous Counts in All Race (ExAC)
7852
Allele Frequency in All Race (ExAC)
0.34957152274225445
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