chr22:29121019:G>A Detail (hg19) (CHEK2)

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Summary
Information
Links
Disease area statistics
MGeND
ClinVar
CIViC
DisGeNET
Annotation
Genome browser

Information

Genome

Assembly	Position
hg19	chr22:29,121,019-29,121,019
hg38	chr22:28,725,031-28,725,031 View the variant detail on this assembly version.

HGVS

CHEK2

Type	Transcript	Protein
RefSeq	NM_001005735.1:c.667C>T	NP_001005735.1:p.Arg223Cys
	NM_001257387.1:c.538C>T	NP_001244316.1:p.Arg180Cys
	NM_145862.2:c.538C>T	NP_665861.1:p.Arg180Cys
Ensemble	ENST00000403642.5:c.320-5546C>T
	ENST00000404276.6:c.538C>T	ENST00000404276.6:p.Arg180Cys
	ENST00000382580.6:c.667C>T	ENST00000382580.6:p.Arg223Cys
	ENST00000402731.6:c.445-108C>T
	ENST00000425190.7:c.-126C>T
	ENST00000405598.5:c.538C>T	ENST00000405598.5:p.Arg180Cys
	ENST00000348295.7:c.538C>T	ENST00000348295.7:p.Arg180Cys
	ENST00000649563.1:c.-71-5546C>T
	ENST00000650281.1:c.538C>T	ENST00000650281.1:p.Arg180Cys

Summary

MGeND

Clinical significance	Pathogenic Uncertain significance
Variant entry	30
GWAS entry
Disease area statistics	Show details

Frequency

JP	HGVD:0.003
	ToMMo:0.001
	NCBN:[No Data.]
	NCBN(Hondo):[No Data.]
	NCBN(Ryukyu):[No Data.]
East asia	ExAC:0.004

Prediction

ClinVar

Clinical Significance	Conflicting classifications of pathogenicity
Review star
Show details

Links

CHEK2

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	tgv65644201	TogoVar
	COSMIC
	MONDO

Disease area statistics

MGeND

Clinical significance	Last evaluated	Condition	Origin	Submission ID	Submitter	Institute	Citation
Uncertain significance	2018/05/14	colon, unspecified	germline	MGS000029 (TMGS000133)	Hitoshi Nakagama	National Cancer Center Japan
Uncertain significance	2018/05/27	ascending colon	germline	MGS000029 (TMGS000133)	Hitoshi Nakagama	National Cancer Center Japan
Uncertain significance	2018/05/14	familial adenomatous polyposis	germline	MGS000029 (TMGS000133)	Hitoshi Nakagama	National Cancer Center Japan
Uncertain significance	2018/05/27	sigmoid colon	germline	MGS000029 (TMGS000133)	Hitoshi Nakagama	National Cancer Center Japan
Uncertain significance	2019/06/23	breast, unspecified	germline	MGS000029 (TMGS000133)	Hitoshi Nakagama	National Cancer Center Japan
Uncertain significance	2018/05/14	sigmoid colon	germline	MGS000029 (TMGS000133)	Hitoshi Nakagama	National Cancer Center Japan
Uncertain significance	2018/01/13	breast, unspecified	germline	MGS000028 (TMGS000049)	Yukihide Momozawa	RIKEN	30287823
Pathogenic		Ovary	germline	MGS000038 (TMGS000091)	Manabu Muto Ichiro Kinoshita	Kyoto University Department of Medical Oncology Faculty of Medicine and Graduate School of Medicine Hokkaido University
Uncertain significance	2021/03/19	prostate	germline	MGS000049 (TMGS000113)	Yukihide Momozawa Koichi Matsuda	RIKEN The University of Tokyo

Past history: no past history; Family history: breast; Histological type: adenocarcinoma; Gleason grade group: 3; Age range: 10-59; (1)
Past history: no past history; Family history: colorectal; Histological type: adenocarcinoma; Gleason grade group: NA; (1)
Past history: no past history; Family history: no family history; Histological type: adenocarcinoma; Gleason grade group: 4; (1)
Past history: no past history; Family history: prostate; Histological type: adenocarcinoma; Gleason grade group: 1; (1)
Past history: no past history; Family history: colorectal; Histological type: adenocarcinoma; Gleason grade group: 3; (1)
Past history: no past history; Family history: no family history; Histological type: adenocarcinoma; Gleason grade group: 5; (1)
Past history: no past history; Family history: gastric; Histological type: adenocarcinoma; Gleason grade group: 1; (1)
Past history: no past history; Family history: no family history; Histological type: adenocarcinoma; Gleason grade group: 1; (2)
Past history: gastric; Family history: gastric; Histological type: adenocarcinoma; Gleason grade group: 2; (1)
Past history: gastric; Family history: no family history; Histological type: adenocarcinoma; Gleason grade group: 2; (1)
Past history: no past history; Family history: gastric; Histological type: others; Gleason grade group: 1; (1)
Past history: no past history; Family history: prostate; Histological type: adenocarcinoma; Gleason grade group: 2; (1)
Past history: no past history; Family history: colorectal; Histological type: NA; Gleason grade group: NA; (1)
Past history: no past history; Family history: prostate; Histological type: NA; Gleason grade group: NA; (1)
Past history: no past history; Family history: bileduct; Histological type: NA; Gleason grade group: NA; (1)
Past history: no past history; Family history: no family history; Histological type: adenocarcinoma; Gleason grade group: 2; (2)
Past history: no past history; Family history: no family history; Histological type: adenocarcinoma; Gleason grade group: NA; Age range: 80-109; (1)
Past history: liver; Family history: no family history; Histological type: adenocarcinoma; Gleason grade group: NA; (1)
Past history: no past history; Family history: no family history; Histological type: adenocarcinoma; Gleason grade group: NA; (1)
Past history: no past history; Family history: prostate; Histological type: adenocarcinoma; Gleason grade group: 4; (1)

ClinVar

Clinical significance	Last evaluated	Review status	Condition	Origin	Links
Conflicting interpretations of pathogenicity	2021-06-09	criteria provided, conflicting interpretations	Hereditary cancer-predisposing syndrome	germline	Detail
Conflicting interpretations of pathogenicity	2024-02-01	criteria provided, conflicting interpretations	Familial cancer of breast	germline unknown	Detail
Uncertain significance	2024-02-06	criteria provided, multiple submitters, no conflicts	not specified	germline	Detail
Uncertain significance	2016-03-18	criteria provided, single submitter	Malignant tumor of prostate	germline	Detail
Conflicting interpretations of pathogenicity	2024-02-01	criteria provided, conflicting interpretations	not provided	germline unknown	Detail
Conflicting interpretations of pathogenicity	2024-01-25	criteria provided, conflicting interpretations	hereditary breast ovarian cancer syndrome	germline	Detail
Uncertain significance	2022-09-14	criteria provided, single submitter	Breast and/or ovarian cancer	germline	Detail
Likely benign	2023-03-28	criteria provided, single submitter	CHEK2-related disorder	germline	Detail
Uncertain significance	2017-04-27	criteria provided, single submitter	CHEK2-related cancer predisposition	germline	Detail

CIViC

[No Data.]

DisGeNET

Score	Disease name	Description	Source	Pubmed	Links
0.138	Malignant neoplasm of prostate	Mutations in CHEK2 associated with prostate cancer risk.	UNIPROT	12533788	Detail

Annotation

Annotations

Descrption	Source	Links
NM_007194.4(CHEK2):c.538C>T (p.Arg180Cys) AND Hereditary cancer-predisposing syndrome	ClinVar	Detail
NM_007194.4(CHEK2):c.538C>T (p.Arg180Cys) AND Familial cancer of breast	ClinVar	Detail
NM_007194.4(CHEK2):c.538C>T (p.Arg180Cys) AND not specified	ClinVar	Detail
NM_007194.4(CHEK2):c.538C>T (p.Arg180Cys) AND Malignant tumor of prostate	ClinVar	Detail
NM_007194.4(CHEK2):c.538C>T (p.Arg180Cys) AND not provided	ClinVar	Detail
NM_007194.4(CHEK2):c.538C>T (p.Arg180Cys) AND Hereditary breast ovarian cancer syndrome	ClinVar	Detail
NM_007194.4(CHEK2):c.538C>T (p.Arg180Cys) AND Breast and/or ovarian cancer	ClinVar	Detail
NM_007194.4(CHEK2):c.538C>T (p.Arg180Cys) AND CHEK2-related disorder	ClinVar	Detail
NM_007194.4(CHEK2):c.538C>T (p.Arg180Cys) AND CHEK2-related cancer predisposition	ClinVar	Detail
Mutations in CHEK2 associated with prostate cancer risk.	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: rs77130927 dbSNP
Genome: hg19
Position: chr22:29,121,019-29,121,019
Variant Type: snv
Reference Allele: G
Alternative Allele: A
Filtering Status (HGVD): PASS
# of samples (HGVD): 1210
Mean of sample read depth (HGVD): 134.76
Standard deviation of sample read depth (HGVD): 58.10
Number of reference allele (HGVD): 2413
Number of alternative allele (HGVD): 7
Allele Frequency (HGVD): 0.002892561983471074
Gene Symbol (HGVD): CHEK2
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)): rs77130927
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 0.001
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 17
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 16760
East Asian Chromosome Counts (ExAC): 8648
East Asian Allele Counts (ExAC): 35
East Asian Heterozygous Counts (ExAC): 35
East Asian Homozygous Counts (ExAC): 0
East Asian Allele Frequency (ExAC): 0.004047178538390379
Chromosome Counts in All Race (ExAC): 121352
Allele Counts in All Race (ExAC): 165
Heterozygous Counts in All Race (ExAC): 165
Homozygous Counts in All Race (ExAC): 0
Allele Frequency in All Race (ExAC): 0.001359680928208847

Genome browser

chr22:29121019:G>A Detail (hg19) (CHEK2)

Genome

HGVS

MGeND

Frequency

Prediction

ClinVar

Clinical information of patient(s) with this variant provided by the submitter(s)

Image provided by the submitter

Annotations

Overlapped Transcript Coordinates

Overlapped Transcript