chr8:90990521:T>C Detail (hg19) (NBN)
Information
Genome
| Assembly | Position |
|---|---|
| hg19 | chr8:90,990,521-90,990,521 |
| hg38 | chr8:89,978,293-89,978,293 View the variant detail on this assembly version. |
HGVS
| Type | Transcript | Protein |
|---|---|---|
| RefSeq | NM_001024688.2:c.265A>G | NP_001019859.1:p.Ile89Val |
| NM_002485.4:c.511A>G | NP_002476.2:p.Ile171Val | |
| Ensemble | ENST00000409330.5:c.265A>G | ENST00000409330.5:p.Ile89Val |
Summary
MGeND
| Clinical significance |
Benign
not provided
|
| Variant entry | 59 |
| 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 | |
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
|
||
|
not provided
|
Primary malignant neoplasm of ovary (disorder) |
unknown
|
MGS000021
(TMGS000080) |
Manabu Muto | Kyoto University | ||||
|
not provided
|
Carcinoma of colon (disorder) |
unknown
|
MGS000021
(TMGS000080) |
Manabu Muto | Kyoto University | ||||
|
not provided
|
Adenocarcinoma of stomach (disorder) |
unknown
|
MGS000021
(TMGS000080) |
Manabu Muto | Kyoto University | ||||
|
not provided
|
Carcinoma of cecum (disorder) |
unknown
|
MGS000021
(TMGS000080) |
Manabu Muto | Kyoto University | ||||
|
not provided
|
Carcinoma of pancreas (disorder) |
unknown
|
MGS000023
(TMGS000082) |
Manabu Muto | Kyoto University | ||||
|
not provided
|
Primary adenocarcinoma of colon (disorder) |
unknown
|
MGS000023
(TMGS000082) |
Manabu Muto | Kyoto University | ||||
|
not provided
|
fundus of stomach |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
body of stomach |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
stomach, unspecified |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
appendix |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
transverse colon |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
descending colon |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
sigmoid colon |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
colon, unspecified |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
malignant neoplasm of rectum |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
head of pancreas |
not provided
|
MGS000042
(TMGS000093) |
Hitoshi Nakagama | National Cancer Center Japan | ||||
|
not provided
|
tail of pancreas |
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 |
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
| Descrption | Source | Links |
|---|---|---|
| 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
- hg19
- Position
- chr8:90,990,521-90,990,521
- 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
- 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
- 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
- Allele Frequency in All Race (ExAC)
- 0.0013941593796403234
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