chr8:89978293:T>C Detail (hg38) (NBN)

Information

Genome

Assembly Position
hg19 chr8:90,990,521-90,990,521 View the variant detail on this assembly version.
hg38 chr8:89,978,293-89,978,293

HGVS

Type Transcript Protein
RefSeq NM_002485.4:c.511A>G NP_002476.2:p.Ile171Val
NM_001024688.2:c.265A>G NP_001019859.1:p.Ile89Val
Ensemble ENST00000265433.8:c.511A>G ENST00000265433.8:p.Ile171Val
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.007
ToMMo:0.006
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.002

Prediction

ClinVar

Clinical Significance Conflicting classifications of pathogenicity
Review star
Show details
Links
Type Database ID Link
Gene MIM 602667 OMIM
HGNC 7652 HGNC
Ensembl ENSG00000104320 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv33898964 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Pathogenic 2004-10-01 no assertion criteria provided aplastic anemia germline Detail
risk factor 2004-10-01 no assertion criteria provided Leukemia, acute lymphoblastic, susceptibility to germline Detail
Conflicting interpretations of pathogenicity 2022-01-24 criteria provided, conflicting interpretations Hereditary cancer-predisposing syndrome germline maternal Detail
Conflicting interpretations of pathogenicity 2019-04-10 criteria provided, conflicting interpretations not specified germline Detail
Conflicting interpretations of pathogenicity 2024-02-01 criteria provided, conflicting interpretations Microcephaly, normal intelligence and immunodeficiency germline Detail
Uncertain significance 2016-03-18 criteria provided, single submitter Acute lymphoid leukemia germline Detail
Conflicting interpretations of pathogenicity 2024-04-01 criteria provided, conflicting interpretations not provided germline unknown Detail
Uncertain significance 2019-05-01 criteria provided, single submitter hereditary breast ovarian cancer syndrome germline Detail
Uncertain significance 2019-01-01 criteria provided, single submitter breast carcinoma unknown Detail
Uncertain significance no assertion criteria provided Carcinoma of colon unknown Detail
Likely benign 2024-01-23 criteria provided, single submitter Hereditary cancer unknown Detail
Likely benign 2023-04-27 criteria provided, single submitter NBN-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.496 Nijmegen breakage syndrome NA CLINVAR Detail
0.120 Neoplastic Syndromes, Hereditary NA CLINVAR Detail
0.194 Malignant neoplasm of breast I171V germline mutation in the NBS1 gene significantly increases risk of breast ... BeFree 17899368 Detail
0.010 breast carcinoma NBS1 variant I171V and breast cancer risk. BeFree 18049891 Detail
<0.001 Hematologic Neoplasms We screened healthy controls and pediatric patients with hematological malignanc... BeFree 15338273 Detail
0.004 Precursor Cell Lymphoblastic Leukemia Lymphoma Four children with acute lymphoblastic leukemia have been reported to be heteroz... BeFree 15338273 Detail
0.001 Acute lymphocytic leukemia Four children with acute lymphoblastic leukemia have been reported to be heteroz... BeFree 15338273 Detail
0.001 Leukemia, Lymphocytic, Acute, L1 A rare polymorphic variant of NBS1 that resulted in an isoleucine to valine subs... BeFree 24830725 Detail
0.010 breast carcinoma I171V germline mutation in the NBS1 gene significantly increases risk of breast ... BeFree 17899368 Detail
0.194 Malignant neoplasm of breast The aim of the study was to analyse the frequency of I171V mutation in NBS1 gene... BeFree 18280732 Detail
0.194 Malignant neoplasm of breast NBS1 variant I171V and breast cancer risk. BeFree 18049891 Detail
0.001 Leukemia, Lymphocytic, Acute, L1 In our previous study we showed that the germline p.I171V mutation in NBN may be... BeFree 24093751 Detail
<0.001 Carcinoma of larynx We have previously shown that the p.I171V NBN gene mutation may contribute to th... BeFree 24079363 Detail
0.001 Congenital chromosomal disease In earlier work, we had identified a remarkable number of structural chromosomal... BeFree 24830725 Detail
0.121 aplastic anemia In earlier work, we had identified a remarkable number of structural chromosomal... BeFree 24830725 Detail
0.121 aplastic anemia NA CLINVAR Detail
<0.001 Solid tumour Is the NBN gene mutation I171V a potential risk factor for malignant solid tumor... BeFree 21436738 Detail
<0.001 Malignant neoplasm of larynx Increased risk of larynx cancer in heterozygous carriers of the I171V mutation o... BeFree 17894553 Detail
0.121 aplastic anemia First case of aplastic anemia in a Japanese child with a homozygous missense mut... BeFree 15338273 Detail
<0.001 Malignant neoplasm of larynx We have previously shown that the p.I171V NBN gene mutation may contribute to th... BeFree 24079363 Detail
0.010 breast carcinoma The aim of the study was to analyse the frequency of I171V mutation in NBS1 gene... BeFree 18280732 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_002485.5(NBN):c.511A>G (p.Ile171Val) AND Aplastic anemia ClinVar Detail
NM_002485.5(NBN):c.511A>G (p.Ile171Val) AND Leukemia, acute lymphoblastic, susceptibility to ClinVar Detail
NM_002485.5(NBN):c.511A>G (p.Ile171Val) AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_002485.5(NBN):c.511A>G (p.Ile171Val) AND not specified ClinVar Detail
NM_002485.5(NBN):c.511A>G (p.Ile171Val) AND Microcephaly, normal intelligence and immunodeficiency ClinVar Detail
NM_002485.5(NBN):c.511A>G (p.Ile171Val) AND Acute lymphoid leukemia ClinVar Detail
NM_002485.5(NBN):c.511A>G (p.Ile171Val) AND not provided ClinVar Detail
NM_002485.5(NBN):c.511A>G (p.Ile171Val) AND Hereditary breast ovarian cancer syndrome ClinVar Detail
NM_002485.5(NBN):c.511A>G (p.Ile171Val) AND Breast carcinoma ClinVar Detail
NM_002485.5(NBN):c.511A>G (p.Ile171Val) AND Carcinoma of colon ClinVar Detail
NM_002485.5(NBN):c.511A>G (p.Ile171Val) AND Hereditary cancer ClinVar Detail
NM_002485.5(NBN):c.511A>G (p.Ile171Val) AND NBN-related disorder ClinVar Detail
NA DisGeNET Detail
NA DisGeNET Detail
I171V germline mutation in the NBS1 gene significantly increases risk of breast cancer. DisGeNET Detail
NBS1 variant I171V and breast cancer risk. DisGeNET Detail
We screened healthy controls and pediatric patients with hematological malignancies and aplastic ane... DisGeNET Detail
Four children with acute lymphoblastic leukemia have been reported to be heterozygous for a germline... DisGeNET Detail
Four children with acute lymphoblastic leukemia have been reported to be heterozygous for a germline... DisGeNET Detail
A rare polymorphic variant of NBS1 that resulted in an isoleucine to valine substitution at amino ac... DisGeNET Detail
I171V germline mutation in the NBS1 gene significantly increases risk of breast cancer. DisGeNET Detail
The aim of the study was to analyse the frequency of I171V mutation in NBS1 gene in 270 women with b... DisGeNET Detail
NBS1 variant I171V and breast cancer risk. DisGeNET Detail
In our previous study we showed that the germline p.I171V mutation in NBN may be considered as a ris... DisGeNET Detail
We have previously shown that the p.I171V NBN gene mutation may contribute to the development of lar... DisGeNET Detail
In earlier work, we had identified a remarkable number of structural chromosomal aberrations in a pa... DisGeNET Detail
In earlier work, we had identified a remarkable number of structural chromosomal aberrations in a pa... DisGeNET Detail
NA DisGeNET Detail
Is the NBN gene mutation I171V a potential risk factor for malignant solid tumors in children? DisGeNET Detail
Increased risk of larynx cancer in heterozygous carriers of the I171V mutation of the NBS1 gene. DisGeNET Detail
First case of aplastic anemia in a Japanese child with a homozygous missense mutation in the NBS1 ge... DisGeNET Detail
We have previously shown that the p.I171V NBN gene mutation may contribute to the development of lar... DisGeNET Detail
The aim of the study was to analyse the frequency of I171V mutation in NBS1 gene in 270 women with b... 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
rs61754966 dbSNP
Genome
hg38
Position
chr8:89,978,293-89,978,293
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
54.38
Standard deviation of sample read depth (HGVD)
25.79
Number of reference allele (HGVD)
2402
Number of alternative allele (HGVD)
18
Allele Frequency (HGVD)
0.00743801652892562
Gene Symbol (HGVD)
NBN
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))
rs61754966
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0063
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
106
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
Chromosome Counts in All Race (ExAC)
121220
Allele Counts in All Race (ExAC)
169
Heterozygous Counts in All Race (ExAC)
169
Homozygous Counts in All Race (ExAC)
0
East Asian Chromosome Counts (ExAC)
8654
East Asian Allele Counts (ExAC)
16
East Asian Heterozygous Counts (ExAC)
16
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.0018488560203374163
Allele Frequency in All Race (ExAC)
0.0013941593796403234
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