chr22:29121087:A>G Detail (hg19) (CHEK2)

Information

Genome

Assembly Position
hg19 chr22:29,121,087-29,121,087
hg38 chr22:28,725,099-28,725,099 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001257387.1:c.470T>C NP_001244316.1:p.Ile157Thr
NM_145862.2:c.470T>C NP_665861.1:p.Ile157Thr
NM_001005735.1:c.599T>C NP_001005735.1:p.Ile200Thr
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

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

Prediction

ClinVar

Clinical Significance Conflicting classifications of pathogenicity; risk factor
Review star
Show details
Links
Type Database ID Link
Gene MIM 604373 OMIM
HGNC 16627 HGNC
Ensembl ENSG00000183765 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv65644255 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Pathogenic Established risk allele 2023-10-30 no assertion criteria provided Li-Fraumeni syndrome 2 unknown germline Detail
Conflicting interpretations of pathogenicity 2023-05-04 criteria provided, conflicting interpretations Hereditary cancer-predisposing syndrome paternal germline maternal Detail
Uncertain significance 2024-02-26 criteria provided, multiple submitters, no conflicts not specified germline Detail
Conflicting interpretations of pathogenicity 2024-01-31 criteria provided, conflicting interpretations Familial cancer of breast unknown germline Detail
Likely pathogenic 2018-05-03 criteria provided, multiple submitters, no conflicts Breast and colorectal cancer, susceptibility to germline Detail
Conflicting interpretations of pathogenicity; risk factor 2024-04-01 criteria provided, conflicting interpretations not provided unknown germline Detail
Uncertain significance 2017-01-01 criteria provided, single submitter Adrenal cortex carcinoma unknown Detail
Uncertain significance no assertion criteria provided unknown Detail
Uncertain significance 2023-04-25 criteria provided, single submitter Breast and/or ovarian cancer germline Detail
Likely pathogenic 2022-01-14 criteria provided, single submitter Li-Fraumeni syndrome 2,Familial cancer of breast,Malignant tumor of prostate,bone osteosarcoma germline Detail
Likely pathogenic 2022-01-14 criteria provided, single submitter Li-Fraumeni syndrome 2,Familial cancer of breast,Malignant tumor of prostate,bone osteosarcoma germline Detail
Likely pathogenic 2022-01-14 criteria provided, single submitter Li-Fraumeni syndrome 2,Familial cancer of breast,Malignant tumor of prostate,bone osteosarcoma germline Detail
Likely pathogenic 2022-01-14 criteria provided, single submitter Li-Fraumeni syndrome 2,Familial cancer of breast,Malignant tumor of prostate,bone osteosarcoma germline Detail
Likely pathogenic 2022-03-22 criteria provided, single submitter Predisposition to cancer germline Detail
Likely pathogenic 2022-01-28 criteria provided, single submitter Li-Fraumeni syndrome 2,colorectal cancer,bone osteosarcoma,Malignant tumor of prostate,Familial cancer of breast germline Detail
Likely pathogenic 2022-01-28 criteria provided, single submitter Li-Fraumeni syndrome 2,colorectal cancer,bone osteosarcoma,Malignant tumor of prostate,Familial cancer of breast germline Detail
Likely pathogenic 2022-01-28 criteria provided, single submitter Li-Fraumeni syndrome 2,colorectal cancer,bone osteosarcoma,Malignant tumor of prostate,Familial cancer of breast germline Detail
Likely pathogenic 2022-01-28 criteria provided, single submitter Li-Fraumeni syndrome 2,colorectal cancer,bone osteosarcoma,Malignant tumor of prostate,Familial cancer of breast germline Detail
Likely pathogenic 2022-01-28 criteria provided, single submitter Li-Fraumeni syndrome 2,colorectal cancer,bone osteosarcoma,Malignant tumor of prostate,Familial cancer of breast germline Detail
Pathogenic 2006-11-01 no assertion criteria provided TUMOR PREDISPOSITION SYNDROME 4, BREAST/PROSTATE/COLORECTAL germline Detail
Pathogenic 2020-10-07 criteria provided, single submitter Malignant tumor of prostate germline Detail
Likely pathogenic 2023-08-17 criteria provided, single submitter CHEK2-related disorder germline Detail
Pathogenic Likely pathogenic 2022-03-25 criteria provided, multiple submitters, no conflicts CHEK2-related cancer predisposition germline unknown Detail
CIViC
Disease Drug EL ET ED CS VO TR Pubmed Links
prostate cancer B Predisposing Supports Uncertain Significance Rare Germline 3 26629066 Detail
DisGeNET
Score Disease name Description Source Pubmed Links
0.127 Breast Cancer, Familial NA CLINVAR Detail
0.120 Neoplastic Syndromes, Hereditary NA CLINVAR Detail
0.360 Li-Fraumeni syndrome 2 NA CLINVAR Detail
<0.001 Papillary thyroid carcinoma As a result of the study, we identified CHEK2 rs17879961 (OR = 2.2, P = 2.37e-10... BeFree 24599715 Detail
0.130 Malignant neoplasm of lung Rare variants of large effect in BRCA2 and CHEK2 affect risk of lung cancer. GWASCAT 24880342 Detail
Annotation

Annotations

DescrptionSourceLinks
Meta-analysis of 4 retrospective studies linked CHEK2 I157T to a higher risk of prostate cancer (OR ... CIViC Evidence Detail
NM_007194.4(CHEK2):c.470T>C (p.Ile157Thr) AND Li-Fraumeni syndrome 2 ClinVar Detail
NM_007194.4(CHEK2):c.470T>C (p.Ile157Thr) AND Hereditary cancer-predisposing syndrome ClinVar Detail
NM_007194.4(CHEK2):c.470T>C (p.Ile157Thr) AND not specified ClinVar Detail
NM_007194.4(CHEK2):c.470T>C (p.Ile157Thr) AND Familial cancer of breast ClinVar Detail
NM_007194.4(CHEK2):c.470T>C (p.Ile157Thr) AND Breast and colorectal cancer, susceptibility to ClinVar Detail
NM_007194.4(CHEK2):c.470T>C (p.Ile157Thr) AND not provided ClinVar Detail
NM_007194.4(CHEK2):c.470T>C (p.Ile157Thr) AND multiple conditions ClinVar Detail
NM_007194.4(CHEK2):c.470T>C (p.Ile157Thr) AND Malignant tumor of breast ClinVar Detail
NM_007194.4(CHEK2):c.470T>C (p.Ile157Thr) AND Breast and/or ovarian cancer ClinVar Detail
NM_007194.4(CHEK2):c.470T>C (p.Ile157Thr) AND multiple conditions ClinVar Detail
NM_007194.4(CHEK2):c.470T>C (p.Ile157Thr) AND multiple conditions ClinVar Detail
NM_007194.4(CHEK2):c.470T>C (p.Ile157Thr) AND multiple conditions ClinVar Detail
NM_007194.4(CHEK2):c.470T>C (p.Ile157Thr) AND multiple conditions ClinVar Detail
NM_007194.4(CHEK2):c.470T>C (p.Ile157Thr) AND Predisposition to cancer ClinVar Detail
NM_007194.4(CHEK2):c.470T>C (p.Ile157Thr) AND multiple conditions ClinVar Detail
NM_007194.4(CHEK2):c.470T>C (p.Ile157Thr) AND multiple conditions ClinVar Detail
NM_007194.4(CHEK2):c.470T>C (p.Ile157Thr) AND multiple conditions ClinVar Detail
NM_007194.4(CHEK2):c.470T>C (p.Ile157Thr) AND multiple conditions ClinVar Detail
NM_007194.4(CHEK2):c.470T>C (p.Ile157Thr) AND multiple conditions ClinVar Detail
NM_007194.4(CHEK2):c.470T>C (p.Ile157Thr) AND TUMOR PREDISPOSITION SYNDROME 4, BREAST/PROSTATE/COLOR... ClinVar Detail
NM_007194.4(CHEK2):c.470T>C (p.Ile157Thr) AND Malignant tumor of prostate ClinVar Detail
NM_007194.4(CHEK2):c.470T>C (p.Ile157Thr) AND CHEK2-related disorder ClinVar Detail
NM_007194.4(CHEK2):c.470T>C (p.Ile157Thr) AND CHEK2-related cancer predisposition ClinVar Detail
NA DisGeNET Detail
NA DisGeNET Detail
NA DisGeNET Detail
As a result of the study, we identified CHEK2 rs17879961 (OR = 2.2, P = 2.37e-10) and BRCA1 rs16941 ... DisGeNET Detail
Rare variants of large effect in BRCA2 and CHEK2 affect risk of lung cancer. 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
rs17879961 dbSNP
Genome
hg19
Position
chr22:29,121,087-29,121,087
Variant Type
snv
Reference Allele
A
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
137.82
Standard deviation of sample read depth (HGVD)
61.84
Number of reference allele (HGVD)
2419
Number of alternative allele (HGVD)
1
Allele Frequency (HGVD)
4.1322314049586776E-4
Gene Symbol (HGVD)
CHEK2
East Asian Chromosome Counts (ExAC)
8654
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)
121350
Allele Counts in All Race (ExAC)
497
Heterozygous Counts in All Race (ExAC)
485
Homozygous Counts in All Race (ExAC)
6
Allele Frequency in All Race (ExAC)
0.0040955912649361355
Variant (CIViC) (CIViC Variant)
I157T
Transcript 1 (CIViC Variant)
ENST00000328354.6
Variant URL (CIViC Variant)
https://civic.genome.wustl.edu/links/variants/787
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