chr17:41244936:G>A Detail (hg19) (BRCA1)

Information

Genome

Assembly Position
hg19 chr17:41,244,936-41,244,936
hg38 chr17:43,092,919-43,092,919 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_007298.3:c.787+1825C>T
NM_007297.3:c.2471C>T NP_009228.2:p.Pro824Leu
NM_007300.3:c.2612C>T NP_009231.2:p.Pro871Leu
Summary

MGeND

Clinical significance Benign Likely benign Uncertain significance
Variant entry 3,771
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:0.378

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 tgv57843654 TogoVar
COSMIC COSM148278 COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
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 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 2015-08-10 reviewed by expert panel Breast-ovarian cancer, familial, susceptibility to, 1 germline not provided unknown Detail
Benign 2020-05-03 criteria provided, multiple submitters, no conflicts Familial cancer of breast germline unknown 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 2024-02-01 criteria provided, multiple submitters, no conflicts hereditary breast ovarian cancer syndrome germline Detail
Benign 2019-04-22 criteria provided, single submitter breast carcinoma germline Detail
Benign 2022-05-06 criteria provided, single submitter Pancreatic cancer, susceptibility to, 4,Breast-ovarian cancer, familial, susceptibility to, 1,Fanconi anemia, complementation group S,Familial cancer of breast unknown Detail
Benign 2022-05-06 criteria provided, single submitter Pancreatic cancer, susceptibility to, 4,Breast-ovarian cancer, familial, susceptibility to, 1,Fanconi anemia, complementation group S,Familial cancer of breast unknown Detail
Benign 2022-05-06 criteria provided, single submitter Pancreatic cancer, susceptibility to, 4,Breast-ovarian cancer, familial, susceptibility to, 1,Fanconi anemia, complementation group S,Familial cancer of breast unknown Detail
Benign 2022-05-06 criteria provided, single submitter Pancreatic cancer, susceptibility to, 4,Breast-ovarian cancer, familial, susceptibility to, 1,Fanconi anemia, complementation group S,Familial cancer of breast unknown Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 Malignant tumor of cervix We genotyped 4 single nucleotide polymorphisms (SNPs) with amino acid changes, T... BeFree 19482343 Detail
0.003 cervix carcinoma We genotyped 4 single nucleotide polymorphisms (SNPs) with amino acid changes, T... BeFree 19482343 Detail
<0.001 Lymphoma, Large-Cell, Follicular Compared to those with BMI &lt;25, women with BMI ≥25 had significantly increase... BeFree 23619945 Detail
0.005 Lymphoma, Non-Hodgkin Compared to those with BMI &lt;25, women with BMI ≥25 had significantly increase... BeFree 23619945 Detail
0.008 Lymphoma, Non-Hodgkin Compared to those with BMI &lt;25, women with BMI ≥25 had significantly increase... BeFree 23619945 Detail
<0.001 Lymphoma, Large-Cell, Follicular Compared to those with BMI &lt;25, women with BMI ≥25 had significantly increase... BeFree 23619945 Detail
<0.001 Lymphoma, Large-Cell, Follicular Compared to those with BMI &lt;25, women with BMI ≥25 had significantly increase... BeFree 23619945 Detail
0.013 Lymphoma, Non-Hodgkin Compared to those with BMI &lt;25, women with BMI ≥25 had significantly increase... BeFree 23619945 Detail
0.006 Lymphoma, Non-Hodgkin Compared to those with BMI &lt;25, women with BMI ≥25 had significantly increase... BeFree 23619945 Detail
<0.001 Lymphoma, Large-Cell, Follicular Compared to those with BMI &lt;25, women with BMI ≥25 had significantly increase... BeFree 23619945 Detail
0.032 Epithelial ovarian cancer No association was detected between EOC risk and BRCA1 Q356R, BRCA1 P871L, RAD51... BeFree 15924337 Detail
0.080 breast carcinoma In this case-control study of 1,004 breast cancer cases and 1,008 controls, we t... BeFree 19205873 Detail
0.360 Malignant neoplasm of breast In this case-control study of 1,004 breast cancer cases and 1,008 controls, we t... BeFree 19205873 Detail
0.010 Malignant neoplasm of breast In this case-control study of 1,004 breast cancer cases and 1,008 controls, we t... BeFree 19205873 Detail
0.003 breast carcinoma In this case-control study of 1,004 breast cancer cases and 1,008 controls, we t... BeFree 19205873 Detail
0.360 Malignant neoplasm of breast To assess whether target SNPs are implicated in BC susceptibility, we conducted ... BeFree 20332227 Detail
0.080 breast carcinoma To assess whether target SNPs are implicated in BC susceptibility, we conducted ... BeFree 20332227 Detail
0.004 Malignant neoplasm of stomach The functional BRCA1 rs799917 genetic polymorphism is associated with gastric ca... BeFree 25266802 Detail
0.004 stomach carcinoma The functional BRCA1 rs799917 genetic polymorphism is associated with gastric ca... BeFree 25266802 Detail
0.080 breast carcinoma Association between BRCA1 rs799917 polymorphism and breast cancer risk: A meta-a... BeFree 25194442 Detail
0.360 Malignant neoplasm of breast Association between BRCA1 rs799917 polymorphism and breast cancer risk: A meta-a... BeFree 25194442 Detail
0.003 cervix carcinoma These findings indicate that BRCA1 rs799917 polymorphism may contribute to the r... BeFree 19482343 Detail
<0.001 Malignant tumor of cervix These findings indicate that BRCA1 rs799917 polymorphism may contribute to the r... BeFree 19482343 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_007294.4(BRCA1):c.2612C>T (p.Pro871Leu) AND not provided ClinVar Detail
NM_007294.4(BRCA1):c.2612C>T (p.Pro871Leu) AND Breast-ovarian cancer, familial, susceptibility to, 1 ClinVar Detail
NM_007294.4(BRCA1):c.2612C>T (p.Pro871Leu) AND Familial cancer of breast ClinVar Detail
NM_007294.4(BRCA1):c.2612C>T (p.Pro871Leu) AND not specified ClinVar Detail
NM_007294.4(BRCA1):c.2612C>T (p.Pro871Leu) AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_007294.4(BRCA1):c.2612C>T (p.Pro871Leu) AND Hereditary breast ovarian cancer syndrome ClinVar Detail
NM_007294.4(BRCA1):c.2612C>T (p.Pro871Leu) AND Breast carcinoma ClinVar Detail
NM_007294.4(BRCA1):c.2612C>T (p.Pro871Leu) AND multiple conditions ClinVar Detail
NM_007294.4(BRCA1):c.2612C>T (p.Pro871Leu) AND multiple conditions ClinVar Detail
NM_007294.4(BRCA1):c.2612C>T (p.Pro871Leu) AND multiple conditions ClinVar Detail
NM_007294.4(BRCA1):c.2612C>T (p.Pro871Leu) AND multiple conditions ClinVar Detail
We genotyped 4 single nucleotide polymorphisms (SNPs) with amino acid changes, TP53 Pro72Arg (rs1042... DisGeNET Detail
We genotyped 4 single nucleotide polymorphisms (SNPs) with amino acid changes, TP53 Pro72Arg (rs1042... DisGeNET Detail
Compared to those with BMI &lt;25, women with BMI ≥25 had significantly increased risk of NHL among ... DisGeNET Detail
Compared to those with BMI &lt;25, women with BMI ≥25 had significantly increased risk of NHL among ... DisGeNET Detail
Compared to those with BMI &lt;25, women with BMI ≥25 had significantly increased risk of NHL among ... DisGeNET Detail
Compared to those with BMI &lt;25, women with BMI ≥25 had significantly increased risk of NHL among ... DisGeNET Detail
Compared to those with BMI &lt;25, women with BMI ≥25 had significantly increased risk of NHL among ... DisGeNET Detail
Compared to those with BMI &lt;25, women with BMI ≥25 had significantly increased risk of NHL among ... DisGeNET Detail
Compared to those with BMI &lt;25, women with BMI ≥25 had significantly increased risk of NHL among ... DisGeNET Detail
Compared to those with BMI &lt;25, women with BMI ≥25 had significantly increased risk of NHL among ... DisGeNET Detail
No association was detected between EOC risk and BRCA1 Q356R, BRCA1 P871L, RAD51 g135c, RAD51 g172t,... DisGeNET Detail
In this case-control study of 1,004 breast cancer cases and 1,008 controls, we tested the hypothesis... DisGeNET Detail
In this case-control study of 1,004 breast cancer cases and 1,008 controls, we tested the hypothesis... DisGeNET Detail
In this case-control study of 1,004 breast cancer cases and 1,008 controls, we tested the hypothesis... DisGeNET Detail
In this case-control study of 1,004 breast cancer cases and 1,008 controls, we tested the hypothesis... DisGeNET Detail
To assess whether target SNPs are implicated in BC susceptibility, we conducted a case-control popul... DisGeNET Detail
To assess whether target SNPs are implicated in BC susceptibility, we conducted a case-control popul... DisGeNET Detail
The functional BRCA1 rs799917 genetic polymorphism is associated with gastric cancer risk in a Chine... DisGeNET Detail
The functional BRCA1 rs799917 genetic polymorphism is associated with gastric cancer risk in a Chine... DisGeNET Detail
Association between BRCA1 rs799917 polymorphism and breast cancer risk: A meta-analysis of 19,878 su... DisGeNET Detail
Association between BRCA1 rs799917 polymorphism and breast cancer risk: A meta-analysis of 19,878 su... DisGeNET Detail
These findings indicate that BRCA1 rs799917 polymorphism may contribute to the risk of cervical canc... DisGeNET Detail
These findings indicate that BRCA1 rs799917 polymorphism may contribute to the risk of cervical canc... 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
rs799917 dbSNP
Genome
hg19
Position
chr17:41,244,936-41,244,936
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1205
Mean of sample read depth (HGVD)
64.85
Standard deviation of sample read depth (HGVD)
38.52
Number of reference allele (HGVD)
1613
Number of alternative allele (HGVD)
797
Allele Frequency (HGVD)
0.33070539419087136
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))
rs799917
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.3276
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
5491
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8642
East Asian Allele Counts (ExAC)
3267
East Asian Heterozygous Counts (ExAC)
1993
East Asian Homozygous Counts (ExAC)
637
East Asian Allele Frequency (ExAC)
0.37803749132145337
Chromosome Counts in All Race (ExAC)
121356
Allele Counts in All Race (ExAC)
49762
Heterozygous Counts in All Race (ExAC)
26590
Homozygous Counts in All Race (ExAC)
11586
Allele Frequency in All Race (ExAC)
0.4100497709219157
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