chr13:32903606:GT> Detail (hg19) (BRCA2)

Information

Genome

Assembly Position
hg19 chr13:32,903,606-32,903,607
hg38 chr13:32,329,469-32,329,470 

HGVS

Type Transcript Protein
RefSeq NM_000059.3:c.658_659delGT NP_000050.2:p.Val220IlefsTer4
Ensemble ENST00000380152.8:c.658_659delGT ENST00000380152.8:p.Val220IlefsTer4
ENST00000530893.7:c.289_290delGT ENST00000530893.7:p.Val97IlefsTer4
Summary

MGeND

Clinical significance Pathogenic not provided
Variant entry 4
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:<0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:<0.001

Prediction

ClinVar

Clinical Significance Pathogenic
Review star
Show details
Links
Type Database ID Link
Gene MIM 600185 OMIM
HGNC 1101 HGNC
Ensembl ENSG00000139618 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv48209357 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Pathogenic 2018/01/13 breast, unspecified germline MGS000028
(TMGS000049) 		Yukihide Momozawa RIKEN 30287823
not provided Biliary cancer somatic MGS000018
(TMGS000110) 		Hitoshi Nakagama National Cancer Center Japan 30742731
Pathogenic 2021/03/19 breast germline MGS000048
(TMGS000112) 		Yukihide Momozawa
Koichi Matsuda		 RIKEN
The University of Tokyo
Pathogenic 2020/04/20 malignant neoplasm of gallbladder not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Pathogenic 2007-01-01 no assertion criteria provided Fanconi anemia complementation group D1 germline Detail
Pathogenic 2021-10-29 criteria provided, single submitter Wilms tumor 1 germline inherited Detail
risk factor 2007-01-01 no assertion criteria provided Glioma susceptibility 3 germline Detail
Pathogenic 2021-10-29 criteria provided, single submitter medulloblastoma germline inherited Detail
Pathogenic 2016-04-22 reviewed by expert panel Breast-ovarian cancer, familial, susceptibility to, 2 germline inherited not provided unknown Detail
Pathogenic 2024-01-29 criteria provided, multiple submitters, no conflicts hereditary breast ovarian cancer syndrome germline Detail
Pathogenic 2023-12-01 criteria provided, multiple submitters, no conflicts not provided germline unknown Detail
Pathogenic 2023-04-11 criteria provided, multiple submitters, no conflicts Hereditary cancer-predisposing syndrome germline Detail
Pathogenic 2020-04-02 criteria provided, multiple submitters, no conflicts Breast-ovarian cancer, familial, susceptibility to, 1 germline Detail
Pathogenic 2021-10-29 criteria provided, multiple submitters, no conflicts Familial cancer of breast germline inherited Detail
Pathogenic 2019-06-11 no assertion criteria provided Breast and/or ovarian cancer germline Detail
Pathogenic no assertion criteria provided unknown Detail
Pathogenic 2021-10-29 criteria provided, single submitter Malignant tumor of prostate inherited Detail
Pathogenic 2021-10-29 criteria provided, single submitter Wilms tumor 1,Pancreatic cancer, susceptibility to, 2,Breast-ovarian cancer, familial, susceptibility to, 2,Familial cancer of breast,Glioma susceptibility 3,medulloblastoma,Fanconi anemia complementation group D1,Malignant tumor of prostate unknown Detail
Pathogenic 2021-10-29 criteria provided, single submitter Wilms tumor 1,Pancreatic cancer, susceptibility to, 2,Breast-ovarian cancer, familial, susceptibility to, 2,Familial cancer of breast,Glioma susceptibility 3,medulloblastoma,Fanconi anemia complementation group D1,Malignant tumor of prostate unknown Detail
Pathogenic 2021-10-29 criteria provided, single submitter Wilms tumor 1,Pancreatic cancer, susceptibility to, 2,Breast-ovarian cancer, familial, susceptibility to, 2,Familial cancer of breast,Glioma susceptibility 3,medulloblastoma,Fanconi anemia complementation group D1,Malignant tumor of prostate unknown Detail
Pathogenic 2021-10-29 criteria provided, single submitter Wilms tumor 1,Pancreatic cancer, susceptibility to, 2,Breast-ovarian cancer, familial, susceptibility to, 2,Familial cancer of breast,Glioma susceptibility 3,medulloblastoma,Fanconi anemia complementation group D1,Malignant tumor of prostate unknown Detail
Pathogenic 2021-10-29 criteria provided, single submitter Wilms tumor 1,Pancreatic cancer, susceptibility to, 2,Breast-ovarian cancer, familial, susceptibility to, 2,Familial cancer of breast,Glioma susceptibility 3,medulloblastoma,Fanconi anemia complementation group D1,Malignant tumor of prostate unknown Detail
Pathogenic 2021-10-29 criteria provided, single submitter Wilms tumor 1,Pancreatic cancer, susceptibility to, 2,Breast-ovarian cancer, familial, susceptibility to, 2,Familial cancer of breast,Glioma susceptibility 3,medulloblastoma,Fanconi anemia complementation group D1,Malignant tumor of prostate unknown Detail
Pathogenic 2021-10-29 criteria provided, single submitter Wilms tumor 1,Pancreatic cancer, susceptibility to, 2,Breast-ovarian cancer, familial, susceptibility to, 2,Familial cancer of breast,Glioma susceptibility 3,medulloblastoma,Fanconi anemia complementation group D1,Malignant tumor of prostate unknown Detail
Pathogenic 2021-10-29 criteria provided, single submitter Wilms tumor 1,Pancreatic cancer, susceptibility to, 2,Breast-ovarian cancer, familial, susceptibility to, 2,Familial cancer of breast,Glioma susceptibility 3,medulloblastoma,Fanconi anemia complementation group D1,Malignant tumor of prostate unknown Detail
Pathogenic 2023-02-21 no assertion criteria provided uterine corpus cancer germline Detail
Pathogenic 2021-07-01 no assertion criteria provided Gastric cancer germline Detail
Pathogenic 2023-07-25 criteria provided, multiple submitters, no conflicts BRCA2-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.240 Breast-ovarian cancer, familial, susceptibility to, 2 NA CLINVAR Detail
0.174 Breast Cancer, Familial NA CLINVAR Detail
0.391 Hereditary Breast and Ovarian Cancer Syndrome NA CLINVAR Detail
0.128 Neoplastic Syndromes, Hereditary NA CLINVAR Detail
0.560 FANCONI ANEMIA, COMPLEMENTATION GROUP D1 NA CLINVAR Detail
0.120 Glioma susceptibility 3 NA CLINVAR Detail
0.241 medulloblastoma NA CLINVAR Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000059.4(BRCA2):c.658_659del (p.Val220fs) AND Fanconi anemia complementation group D1 ClinVar Detail
NM_000059.4(BRCA2):c.658_659del (p.Val220fs) AND Wilms tumor 1 ClinVar Detail
NM_000059.4(BRCA2):c.658_659del (p.Val220fs) AND Glioma susceptibility 3 ClinVar Detail
NM_000059.4(BRCA2):c.658_659del (p.Val220fs) AND Medulloblastoma ClinVar Detail
NM_000059.4(BRCA2):c.658_659del (p.Val220fs) AND Breast-ovarian cancer, familial, susceptibility to,... ClinVar Detail
NM_000059.4(BRCA2):c.658_659del (p.Val220fs) AND Hereditary breast ovarian cancer syndrome ClinVar Detail
NM_000059.4(BRCA2):c.658_659del (p.Val220fs) AND not provided ClinVar Detail
NM_000059.4(BRCA2):c.658_659del (p.Val220fs) AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_000059.4(BRCA2):c.658_659del (p.Val220fs) AND Breast-ovarian cancer, familial, susceptibility to,... ClinVar Detail
NM_000059.4(BRCA2):c.658_659del (p.Val220fs) AND Familial cancer of breast ClinVar Detail
NM_000059.4(BRCA2):c.658_659del (p.Val220fs) AND Breast and/or ovarian cancer ClinVar Detail
NM_000059.4(BRCA2):c.658_659del (p.Val220fs) AND Malignant tumor of breast ClinVar Detail
NM_000059.4(BRCA2):c.658_659del (p.Val220fs) AND Malignant tumor of prostate ClinVar Detail
NM_000059.4(BRCA2):c.658_659del (p.Val220fs) AND multiple conditions ClinVar Detail
NM_000059.4(BRCA2):c.658_659del (p.Val220fs) AND multiple conditions ClinVar Detail
NM_000059.4(BRCA2):c.658_659del (p.Val220fs) AND multiple conditions ClinVar Detail
NM_000059.4(BRCA2):c.658_659del (p.Val220fs) AND multiple conditions ClinVar Detail
NM_000059.4(BRCA2):c.658_659del (p.Val220fs) AND multiple conditions ClinVar Detail
NM_000059.4(BRCA2):c.658_659del (p.Val220fs) AND multiple conditions ClinVar Detail
NM_000059.4(BRCA2):c.658_659del (p.Val220fs) AND multiple conditions ClinVar Detail
NM_000059.4(BRCA2):c.658_659del (p.Val220fs) AND multiple conditions ClinVar Detail
NM_000059.4(BRCA2):c.658_659del (p.Val220fs) AND Uterine corpus cancer ClinVar Detail
NM_000059.4(BRCA2):c.658_659del (p.Val220fs) AND Gastric cancer ClinVar Detail
NM_000059.4(BRCA2):c.658_659del (p.Val220fs) AND BRCA2-related disorder ClinVar Detail
NA DisGeNET Detail
NA DisGeNET Detail
NA DisGeNET Detail
NA DisGeNET Detail
NA DisGeNET Detail
NA DisGeNET Detail
NA 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
rs80359604 dbSNP
Genome
hg19
Position
chr13:32,903,606-32,903,607
Variant Type
snv
Reference Allele
GT
Alternative Allele
-
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))
rs80359604
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0001
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8156
East Asian Allele Counts (ExAC)
0
East Asian Heterozygous Counts (ExAC)
0
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.0
Chromosome Counts in All Race (ExAC)
98050
Allele Counts in All Race (ExAC)
6
Heterozygous Counts in All Race (ExAC)
6
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
6.119326874043855E-5
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