chr9:27969442:C>T Detail (hg38) (LINGO2)

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

Information

Genome

Assembly	Position
hg19	chr9:27,969,440-27,969,440 View the variant detail on this assembly version.
hg38	chr9:27,969,442-27,969,442

HGVS

LINGO2

Type	Transcript	Protein
RefSeq	NM_001258282.1:c.-35-18736G>A
	NM_152570.2:c.-35-18736G>A
Ensemble	ENST00000379992.6:c.-35-18736G>A
	ENST00000698399.1:c.-35-18736G>A
	ENST00000698400.1:c.-35-18736G>A
	ENST00000698401.1:c.-36+4806G>A
	ENST00000698402.1:c.-35-18736G>A
	ENST00000698403.1:c.-35-18736G>A

Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics	Show details

Frequency

JP	HGVD:[No Data.]
	ToMMo:0.095
	NCBN:[No Data.]
	NCBN(Hondo):[No Data.]
	NCBN(Ryukyu):[No Data.]
East asia	ExAC:[No Data.]

Prediction

ClinVar

Clinical Significance
Review star	[No Data.]
Show details

Links

LINGO2

Type	Database	ID	Link
Gene	MIM	609793	OMIM
	HGNC	21207	HGNC
	Ensembl	ENSG00000174482	Ensembl
	NCBI		NCBI
	Gene Cards		Gene Cards
	OncoKB		OncoKB

Type	Database	ID	Link
Variant	TogoVar	tgv35922654	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	Malignant neoplasm of breast	ASSET analyses identified four SNPs significantly associated with multiple cance...	BeFree	25239644	Detail
0.001	Carcinoma of bladder	ASSET analyses identified four SNPs significantly associated with multiple cance...	BeFree	25239644	Detail
0.001	Carcinoma of lung	ASSET analyses identified four SNPs significantly associated with multiple cance...	BeFree	25239644	Detail
0.001	Malignant neoplasm of lung	ASSET analyses identified four SNPs significantly associated with multiple cance...	BeFree	25239644	Detail
0.001	Malignant neoplasm of urinary bladder	ASSET analyses identified four SNPs significantly associated with multiple cance...	BeFree	25239644	Detail
0.015	Carcinoma of bladder	ASSET analyses identified four SNPs significantly associated with multiple cance...	BeFree	25239644	Detail
<0.001	stomach carcinoma	ASSET analyses identified four SNPs significantly associated with multiple cance...	BeFree	25239644	Detail
0.001	breast carcinoma	ASSET analyses identified four SNPs significantly associated with multiple cance...	BeFree	25239644	Detail
0.038	Malignant neoplasm of lung	ASSET analyses identified four SNPs significantly associated with multiple cance...	BeFree	25239644	Detail
<0.001	Malignant neoplasm of stomach	ASSET analyses identified four SNPs significantly associated with multiple cance...	BeFree	25239644	Detail
0.030	Carcinoma of lung	ASSET analyses identified four SNPs significantly associated with multiple cance...	BeFree	25239644	Detail
0.023	breast carcinoma	ASSET analyses identified four SNPs significantly associated with multiple cance...	BeFree	25239644	Detail
0.043	Malignant neoplasm of breast	ASSET analyses identified four SNPs significantly associated with multiple cance...	BeFree	25239644	Detail
0.022	Malignant neoplasm of urinary bladder	ASSET analyses identified four SNPs significantly associated with multiple cance...	BeFree	25239644	Detail

Annotation

Annotations

Descrption	Source	Links
ASSET analyses identified four SNPs significantly associated with multiple cancers: rs3731239 (CDKN2...	DisGeNET	Detail
ASSET analyses identified four SNPs significantly associated with multiple cancers: rs3731239 (CDKN2...	DisGeNET	Detail
ASSET analyses identified four SNPs significantly associated with multiple cancers: rs3731239 (CDKN2...	DisGeNET	Detail
ASSET analyses identified four SNPs significantly associated with multiple cancers: rs3731239 (CDKN2...	DisGeNET	Detail
ASSET analyses identified four SNPs significantly associated with multiple cancers: rs3731239 (CDKN2...	DisGeNET	Detail
ASSET analyses identified four SNPs significantly associated with multiple cancers: rs3731239 (CDKN2...	DisGeNET	Detail
ASSET analyses identified four SNPs significantly associated with multiple cancers: rs3731239 (CDKN2...	DisGeNET	Detail
ASSET analyses identified four SNPs significantly associated with multiple cancers: rs3731239 (CDKN2...	DisGeNET	Detail
ASSET analyses identified four SNPs significantly associated with multiple cancers: rs3731239 (CDKN2...	DisGeNET	Detail
ASSET analyses identified four SNPs significantly associated with multiple cancers: rs3731239 (CDKN2...	DisGeNET	Detail
ASSET analyses identified four SNPs significantly associated with multiple cancers: rs3731239 (CDKN2...	DisGeNET	Detail
ASSET analyses identified four SNPs significantly associated with multiple cancers: rs3731239 (CDKN2...	DisGeNET	Detail
ASSET analyses identified four SNPs significantly associated with multiple cancers: rs3731239 (CDKN2...	DisGeNET	Detail
ASSET analyses identified four SNPs significantly associated with multiple cancers: rs3731239 (CDKN2...	DisGeNET	Detail

Overlapped Transcript

Gene	Transcript ID	Chromosome	Start	Stop	Links

Gene: -
dbSNP: rs12683422 dbSNP
Genome: hg38
Position: chr9:27,969,442-27,969,442
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)): rs12683422
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 0.0952
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 1595
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 16760

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