chr3:9798140:C>G Detail (hg19) (OGG1)

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

Genome

Assembly	Position
hg19	chr3:9,798,140-9,798,140
hg38	chr3:9,756,456-9,756,456 View the variant detail on this assembly version.

HGVS

OGG1

Type	Transcript	Protein
RefSeq	NM_002542.5:c.748-15C>G
	NM_016820.3:c.748-15C>G
	NM_016828.2:c.748-15C>G
	NM_016821.2:c.748-15C>G
	NM_016819.3:c.748-15C>G
	NM_016829.2:c.748-15C>G
Ensemble	ENST00000302003.11:c.748-15C>G
	ENST00000302008.12:c.748-15C>G
	ENST00000302036.12:c.748-15C>G
	ENST00000339511.9:c.748-15C>G
	ENST00000344629.12:c.748-15C>G
	ENST00000352937.6:c.747+1571C>G
	ENST00000383826.9:c.565+4507C>G
	ENST00000449570.6:c.748-15C>G
	ENST00000707074.1:c.748-311C>G

Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics	Show details

Frequency

JP	HGVD:0.483
	ToMMo:0.466
	NCBN:[No Data.]
	NCBN(Hondo):[No Data.]
	NCBN(Ryukyu):[No Data.]
East asia	ExAC:0.588

Prediction

ClinVar

Clinical Significance
Review star	[No Data.]
Show details

Links

OGG1

Type	Database	ID	Link
Gene	MIM	601982	OMIM
	HGNC	8125	HGNC
	Ensembl	ENSG00000114026	Ensembl
	NCBI		NCBI
	Gene Cards		Gene Cards
	OncoKB		OncoKB

Type	Database	ID	Link
Variant	TogoVar	tgv11422521	TogoVar
	COSMIC
	MONDO

Disease area statistics

[No Data.]

MGeND

[No Data.]

ClinVar

[No Data.]

CIViC

[No Data.]

DisGeNET

Score	Disease name	Description	Source	Pubmed	Links
<0.001	gallbladder carcinoma	Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&...	BeFree	21283657	Detail
<0.001	gallbladder carcinoma	Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&...	BeFree	21283657	Detail
<0.001	gallbladder carcinoma	Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&...	BeFree	21283657	Detail
<0.001	gallbladder carcinoma	Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&...	BeFree	21283657	Detail
<0.001	gallbladder carcinoma	Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&...	BeFree	21283657	Detail
<0.001	Malignant neoplasm of gallbladder	Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&...	BeFree	21283657	Detail
<0.001	Malignant neoplasm of gallbladder	Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&...	BeFree	21283657	Detail
0.001	Malignant neoplasm of gallbladder	Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&...	BeFree	21283657	Detail
<0.001	Malignant neoplasm of gallbladder	Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&...	BeFree	21283657	Detail
<0.001	Malignant neoplasm of gallbladder	Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&...	BeFree	21283657	Detail
0.001	gallbladder carcinoma	Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&...	BeFree	21283657	Detail
<0.001	Malignant neoplasm of gallbladder	Single locus analysis by logistic regression showed association of MSH2 IVS1+9G&...	BeFree	21283657	Detail

Annotation

Annotations

Descrption	Source	Links
Single locus analysis by logistic regression showed association of MSH2 IVS1+9G>C (rs2303426), ER...	DisGeNET	Detail
Single locus analysis by logistic regression showed association of MSH2 IVS1+9G>C (rs2303426), ER...	DisGeNET	Detail
Single locus analysis by logistic regression showed association of MSH2 IVS1+9G>C (rs2303426), ER...	DisGeNET	Detail
Single locus analysis by logistic regression showed association of MSH2 IVS1+9G>C (rs2303426), ER...	DisGeNET	Detail
Single locus analysis by logistic regression showed association of MSH2 IVS1+9G>C (rs2303426), ER...	DisGeNET	Detail
Single locus analysis by logistic regression showed association of MSH2 IVS1+9G>C (rs2303426), ER...	DisGeNET	Detail
Single locus analysis by logistic regression showed association of MSH2 IVS1+9G>C (rs2303426), ER...	DisGeNET	Detail
Single locus analysis by logistic regression showed association of MSH2 IVS1+9G>C (rs2303426), ER...	DisGeNET	Detail
Single locus analysis by logistic regression showed association of MSH2 IVS1+9G>C (rs2303426), ER...	DisGeNET	Detail
Single locus analysis by logistic regression showed association of MSH2 IVS1+9G>C (rs2303426), ER...	DisGeNET	Detail
Single locus analysis by logistic regression showed association of MSH2 IVS1+9G>C (rs2303426), ER...	DisGeNET	Detail
Single locus analysis by logistic regression showed association of MSH2 IVS1+9G>C (rs2303426), ER...	DisGeNET	Detail

Overlapped Transcript

Gene	Transcript ID	Chromosome	Start	Stop	Links

Gene: -
Genome: hg19
Position: chr3:9,798,140-9,798,140
Variant Type: snv
Reference Allele: C
Alternative Allele: G
Filtering Status (HGVD): PASS
# of samples (HGVD): 837
Mean of sample read depth (HGVD): 114.62
Standard deviation of sample read depth (HGVD): 53.64
Number of reference allele (HGVD): 866
Number of alternative allele (HGVD): 808
Allele Frequency (HGVD): 0.4826762246117085
Gene Symbol (HGVD): OGG1
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)): rs2072668
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 0.4661
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 7812
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 16760
East Asian Chromosome Counts (ExAC): 8618
East Asian Allele Counts (ExAC): 5068
East Asian Heterozygous Counts (ExAC): 2068
East Asian Homozygous Counts (ExAC): 1500
East Asian Allele Frequency (ExAC): 0.58807147830123
Chromosome Counts in All Race (ExAC): 121096
Allele Counts in All Race (ExAC): 34030
Heterozygous Counts in All Race (ExAC): 23150
Homozygous Counts in All Race (ExAC): 5440
Allele Frequency in All Race (ExAC): 0.2810167140120235

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