chr13:32914068:TTAA> Detail (hg19) (BRCA2)

Information

Genome

Assembly Position
hg19 chr13:32,914,068-32,914,071
hg38 chr13:32,339,931-32,339,934 

HGVS

Type Transcript Protein
RefSeq NM_000059.3:c.5576_5579delTTAA NP_000050.2:p.Ile1859LysfsTer3
Ensemble ENST00000380152.8:c.5576_5579delTTAA ENST00000380152.8:p.Ile1859LysfsTer3
ENST00000530893.7:c.5207_5210delTTAA ENST00000530893.7:p.Ile1736LysfsTer3
Summary

MGeND

Clinical significance Pathogenic not provided
Variant entry 66
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:<0.001
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 tgv48213309 TogoVar
COSMIC COSM6906194 COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Pathogenic 2019/08/20 hereditary breast and ovarian cancer syndrome germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Pathogenic 2018/11/22 peritoneum, unspecified germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Pathogenic 2019/08/20 breast, unspecified germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Pathogenic 2018/11/22 hereditary breast and ovarian cancer syndrome germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Pathogenic 2018/11/22 breast, unspecified germline MGS000029
(TMGS000133) 		Hitoshi Nakagama National Cancer Center Japan
Pathogenic 2018/01/13 breast, unspecified germline MGS000028
(TMGS000049) 		Yukihide Momozawa RIKEN 30287823
not provided Human epidermal growth factor 2 negative carcinoma of breast (disorder)_Hormone receptor negative neoplasm (disorder) unknown MGS000021
(TMGS000080) 		Manabu Muto Kyoto University
not provided Soft tissue sarcoma germline MGS000018
(TMGS000110) 		Hitoshi Nakagama National Cancer Center Japan 30742731
not provided Breast cancer germline MGS000018
(TMGS000110) 		Hitoshi Nakagama National Cancer Center Japan 30742731
Pathogenic 2021/03/19 control germline MGS000047
(TMGS000111) 		Yukihide Momozawa
Koichi Matsuda		 RIKEN
The University of Tokyo
Pathogenic 2021/03/19 breast germline MGS000048
(TMGS000112) 		Yukihide Momozawa
Koichi Matsuda		 RIKEN
The University of Tokyo
Pathogenic 2021/03/19 prostate germline MGS000049
(TMGS000113) 		Yukihide Momozawa
Koichi Matsuda		 RIKEN
The University of Tokyo
Pathogenic 2021/03/19 Colorectal germline MGS000050
(TMGS000114) 		Yukihide Momozawa
Koichi Matsuda		 RIKEN
The University of Tokyo
Pathogenic 2021/03/19 pancreatic germline MGS000051
(TMGS000115) 		Yukihide Momozawa
Koichi Matsuda		 RIKEN
The University of Tokyo
Pathogenic other germline MGS000001
(TMGS000154) 		Kenjiro Kosaki Keio University
not provided sigmoid colon not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Pathogenic 2020/04/20 bronchus or lung, unspecified not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
not provided bronchus or lung, unspecified not provided MGS000042
(TMGS000093) 		Hitoshi Nakagama National Cancer Center Japan
Pathogenic 2020/04/20 malignant neoplasm of rectum not provided MGS000041
(TMGS000094) 		Hitoshi Nakagama National Cancer Center Japan
Pathogenic 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
Pathogenic 2016-04-22 reviewed by expert panel Breast-ovarian cancer, familial, susceptibility to, 2 germline unknown Detail
Pathogenic 2024-01-28 criteria provided, multiple submitters, no conflicts hereditary breast ovarian cancer syndrome germline Detail
Pathogenic 2023-03-13 criteria provided, multiple submitters, no conflicts Hereditary cancer-predisposing syndrome germline Detail
Pathogenic 2023-11-03 criteria provided, multiple submitters, no conflicts not provided germline unknown Detail
not provided no assertion provided Fanconi anemia complementation group D1,hereditary breast ovarian cancer syndrome unknown Detail
not provided no assertion provided Fanconi anemia complementation group D1,hereditary breast ovarian cancer syndrome unknown Detail
Pathogenic 2009-03-10 no assertion criteria provided Breast and/or ovarian cancer germline Detail
Pathogenic 2023-10-08 criteria provided, single submitter Familial cancer of breast germline unknown Detail
Pathogenic no assertion criteria provided unknown Detail
Pathogenic 2021-07-01 no assertion criteria provided Gastric cancer 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
Annotation

Annotations

DescrptionSourceLinks
NM_000059.4(BRCA2):c.5576_5579del (p.Ile1859fs) AND Breast-ovarian cancer, familial, susceptibility ... ClinVar Detail
NM_000059.4(BRCA2):c.5576_5579del (p.Ile1859fs) AND Hereditary breast ovarian cancer syndrome ClinVar Detail
NM_000059.4(BRCA2):c.5576_5579del (p.Ile1859fs) AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_000059.4(BRCA2):c.5576_5579del (p.Ile1859fs) AND not provided ClinVar Detail
NM_000059.4(BRCA2):c.5576_5579del (p.Ile1859fs) AND multiple conditions ClinVar Detail
NM_000059.4(BRCA2):c.5576_5579del (p.Ile1859fs) AND multiple conditions ClinVar Detail
NM_000059.4(BRCA2):c.5576_5579del (p.Ile1859fs) AND Breast and/or ovarian cancer ClinVar Detail
NM_000059.4(BRCA2):c.5576_5579del (p.Ile1859fs) AND Familial cancer of breast ClinVar Detail
NM_000059.4(BRCA2):c.5576_5579del (p.Ile1859fs) AND Malignant tumor of breast ClinVar Detail
NM_000059.4(BRCA2):c.5576_5579del (p.Ile1859fs) AND Gastric cancer ClinVar 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
rs80359520 dbSNP
Genome
hg19
Position
chr13:32,914,068-32,914,071
Variant Type
snv
Reference Allele
TTAA
Alternative Allele
-
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
75.93
Standard deviation of sample read depth (HGVD)
31.27
Number of reference allele (HGVD)
2419
Number of alternative allele (HGVD)
1
Allele Frequency (HGVD)
4.1322314049586776E-4
Gene Symbol (HGVD)
BRCA2
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))
rs80359520
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))
2
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)
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)
120450
Allele Counts in All Race (ExAC)
4
Heterozygous Counts in All Race (ExAC)
4
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
3.3208800332088E-5
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