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 Benign
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 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 tgv57842804 TogoVar
COSMIC COSM148277 COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Benign Centenarian germline MGS000068
(TMGS000140) 		Kenjiro Kosaki Keio University
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

DescrptionSourceLinks
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
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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