chr22:29121015:C>T 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	chr22:29,121,015-29,121,015
hg38	chr22:28,725,027-28,725,027 View the variant detail on this assembly version.

HGVS

CHEK2

Type	Transcript	Protein
RefSeq	NM_001257387.1:c.542G>A	NP_001244316.1:p.Arg181His
	NM_145862.2:c.542G>A	NP_665861.1:p.Arg181His
	NM_001005735.1:c.671G>A	NP_001005735.1:p.Arg224His
Ensemble	ENST00000425190.7:c.-122G>A
	ENST00000348295.7:c.542G>A	ENST00000348295.7:p.Arg181His
	ENST00000382580.6:c.671G>A	ENST00000382580.6:p.Arg224His
	ENST00000403642.5:c.320-5542G>A
	ENST00000405598.5:c.542G>A	ENST00000405598.5:p.Arg181His
	ENST00000402731.6:c.445-104G>A
	ENST00000404276.6:c.542G>A	ENST00000404276.6:p.Arg181His
	ENST00000650281.1:c.542G>A	ENST00000650281.1:p.Arg181His
	ENST00000649563.1:c.-71-5542G>A

Summary

MGeND

Clinical significance	Benign Uncertain significance
Variant entry	82
GWAS entry
Disease area statistics	Show details

Frequency

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

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	tgv65644196	TogoVar
	COSMIC
	MONDO

Disease area statistics

MGeND

Clinical significance	Last evaluated	Condition	Origin	Submission ID	Submitter	Institute	Citation
Benign	2018/01/13	breast, unspecified	germline	MGS000028 (TMGS000049)	Yukihide Momozawa	RIKEN	30287823
Uncertain significance		NSCLC	germline	MGS000038 (TMGS000091)	Manabu Muto Ichiro Kinoshita	Kyoto University Department of Medical Oncology Faculty of Medicine and Graduate School of Medicine Hokkaido University
Benign	2021/03/19	control	germline	MGS000047 (TMGS000111)	Yukihide Momozawa Koichi Matsuda	RIKEN The University of Tokyo
Benign	2021/03/19	breast	germline	MGS000048 (TMGS000112)	Yukihide Momozawa Koichi Matsuda	RIKEN The University of Tokyo
Uncertain significance	2021/03/19	prostate	germline	MGS000049 (TMGS000113)	Yukihide Momozawa Koichi Matsuda	RIKEN The University of Tokyo
Benign	2021/03/19	Colorectal	germline	MGS000050 (TMGS000114)	Yukihide Momozawa Koichi Matsuda	RIKEN The University of Tokyo
Benign	2021/03/19	pancreatic	germline	MGS000051 (TMGS000115)	Yukihide Momozawa Koichi Matsuda	RIKEN The University of Tokyo

Past history: no past history; Family history: no family history; Histological type: invasive scirrhous carcinoma; ER: NA; PgR: NA; HER2: NA; (2)
Past history: no past history; Family history: breast, colorectal, liver, and lung; Histological type: invasive papillotubular carcinoma; ER: positive; PgR: positive; HER2: negative; (1)
Past history: no past history; Family history: no family history; Histological type: invasive papillotubular carcinoma; ER: negative; PgR: negative; HER2: NA; (1)
Past history: no past history; Family history: no family history; Histological type: invasive scirrhous carcinoma; ER: positive; PgR: positive; HER2: negative; Age range: 10-39; (1)
Past history: no past history; Family history: no family history; Histological type: NA; ER: NA; PgR: NA; HER2: NA; Age range: 10-39; (1)
Past history: no past history; Family history: colorectal; Histological type: invasive papillotubular carcinoma; ER: NA; PgR: NA; HER2: NA; (1)
Past history: no past history; Family history: gastric; Histological type: invasive solid-tubular carcinoma; ER: NA; PgR: NA; HER2: NA; (1)
Past history: no past history; Family history: no family history; Histological type: others; ER: positive; PgR: positive; HER2: negative; (1)
Past history: no past history; Family history: no family history; Histological type: NA; ER: NA; PgR: NA; HER2: NA; (2)
Past history: no past history; Family history: breast; Histological type: invasive papillotubular carcinoma; ER: positive; PgR: positive; HER2: NA; (1)
Past history: no past history; Family history: no family history; Histological type: invasive solid-tubular carcinoma; ER: NA; PgR: NA; HER2: NA; (1)
Past history: no past history; Family history: gastric; Histological type: noninvasive ductal carcinoma; ER: NA; PgR: NA; HER2: NA; (1)
Past history: no past history; Family history: no family history; Histological type: special types; ER: positive; PgR: positive; HER2: negative; (1)
Past history: no past history; Family history: no family history; Histological type: invasive scirrhous carcinoma; ER: positive; PgR: positive; HER2: NA; (1)

ClinVar

Clinical significance	Last evaluated	Review status	Condition	Origin	Links
Conflicting interpretations of pathogenicity	2021-02-10	criteria provided, conflicting interpretations	not provided	germline	Detail
Conflicting interpretations of pathogenicity	2022-09-30	criteria provided, conflicting interpretations	Hereditary cancer-predisposing syndrome	germline	Detail
Uncertain significance	2024-01-19	criteria provided, multiple submitters, no conflicts	Familial cancer of breast	germline unknown	Detail
Uncertain significance	2018-10-31	criteria provided, single submitter	bone osteosarcoma,Li-Fraumeni syndrome 2,Familial cancer of breast,Malignant tumor of prostate	unknown	Detail
Uncertain significance	2018-10-31	criteria provided, single submitter	bone osteosarcoma,Li-Fraumeni syndrome 2,Familial cancer of breast,Malignant tumor of prostate	unknown	Detail
Uncertain significance	2018-10-31	criteria provided, single submitter	bone osteosarcoma,Li-Fraumeni syndrome 2,Familial cancer of breast,Malignant tumor of prostate	unknown	Detail
Uncertain significance	2018-10-31	criteria provided, single submitter	bone osteosarcoma,Li-Fraumeni syndrome 2,Familial cancer of breast,Malignant tumor of prostate	unknown	Detail
Uncertain significance	2019-05-01	criteria provided, single submitter	hereditary breast ovarian cancer syndrome	germline	Detail
Likely benign	2024-02-06	criteria provided, multiple submitters, no conflicts	not specified	germline	Detail
Uncertain significance	2019-05-28	criteria provided, single submitter	Li-Fraumeni syndrome 2	maternal	Detail
Uncertain significance		no assertion criteria provided		unknown	Detail
Likely benign	2022-11-23	criteria provided, single submitter	Breast and/or ovarian cancer	germline	Detail
Pathogenic	2003-02-01	no assertion criteria provided	Malignant tumor of prostate	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
0.120	Neoplastic Syndromes, Hereditary	NA	CLINVAR		Detail
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.542G>A (p.Arg181His) AND not provided	ClinVar	Detail
NM_007194.4(CHEK2):c.542G>A (p.Arg181His) AND Hereditary cancer-predisposing syndrome	ClinVar	Detail
NM_007194.4(CHEK2):c.542G>A (p.Arg181His) AND Familial cancer of breast	ClinVar	Detail
NM_007194.4(CHEK2):c.542G>A (p.Arg181His) AND multiple conditions	ClinVar	Detail
NM_007194.4(CHEK2):c.542G>A (p.Arg181His) AND multiple conditions	ClinVar	Detail
NM_007194.4(CHEK2):c.542G>A (p.Arg181His) AND multiple conditions	ClinVar	Detail
NM_007194.4(CHEK2):c.542G>A (p.Arg181His) AND multiple conditions	ClinVar	Detail
NM_007194.4(CHEK2):c.542G>A (p.Arg181His) AND Hereditary breast ovarian cancer syndrome	ClinVar	Detail
NM_007194.4(CHEK2):c.542G>A (p.Arg181His) AND not specified	ClinVar	Detail
NM_007194.4(CHEK2):c.542G>A (p.Arg181His) AND Li-Fraumeni syndrome 2	ClinVar	Detail
NM_007194.4(CHEK2):c.542G>A (p.Arg181His) AND Malignant tumor of breast	ClinVar	Detail
NM_007194.4(CHEK2):c.542G>A (p.Arg181His) AND Breast and/or ovarian cancer	ClinVar	Detail
NM_007194.4(CHEK2):c.542G>A (p.Arg181His) AND Malignant tumor of prostate	ClinVar	Detail
NM_007194.4(CHEK2):c.542G>A (p.Arg181His) AND CHEK2-related cancer predisposition	ClinVar	Detail
NA	DisGeNET	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: rs121908701 dbSNP
Genome: hg19
Position: chr22:29,121,015-29,121,015
Variant Type: snv
Reference Allele: C
Alternative Allele: T
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)): rs121908701
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 0.0007
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 12
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): 10
East Asian Heterozygous Counts (ExAC): 10
East Asian Homozygous Counts (ExAC): 0
East Asian Allele Frequency (ExAC): 0.001156336725254394
Chromosome Counts in All Race (ExAC): 121350
Allele Counts in All Race (ExAC): 13
Heterozygous Counts in All Race (ExAC): 13
Homozygous Counts in All Race (ExAC): 0
Allele Frequency in All Race (ExAC): 1.0712814173877215E-4

Genome browser

chr22:29121015:C>T Detail (hg19) (CHEK2)

Genome

HGVS

MGeND

Frequency

Prediction

ClinVar

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

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

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

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

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

Image provided by the submitter

Annotations

Overlapped Transcript Coordinates

Overlapped Transcript