chr22:31011610:G>C Detail (hg19) (TCN2)

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

Genome

Assembly	Position
hg19	chr22:31,011,610-31,011,610
hg38	chr22:30,615,623-30,615,623 View the variant detail on this assembly version.

HGVS

TCN2

Type	Transcript	Protein
RefSeq	NM_000355.3:c.776G>C	NP_000346.2:p.Arg259Pro
	NM_001184726.1:c.695G>C	NP_001171655.1:p.Arg232Pro
Ensemble	ENST00000215838.8:c.776G>C	ENST00000215838.8:p.Arg259Pro
	ENST00000405742.7:c.764G>C	ENST00000405742.7:p.Arg255Pro
	ENST00000407817.3:c.695G>C	ENST00000407817.3:p.Arg232Pro
	ENST00000450638.5:c.701G>C	ENST00000450638.5:p.Arg234Pro
	ENST00000698263.1:c.776G>C	ENST00000698263.1:p.Arg259Pro
	ENST00000698265.1:c.776G>C	ENST00000698265.1:p.Arg259Pro
	ENST00000698266.1:c.776G>C	ENST00000698266.1:p.Arg259Pro
	ENST00000698268.1:c.776G>C	ENST00000698268.1:p.Arg259Pro
	ENST00000698270.1:c.623G>C	ENST00000698270.1:p.Arg208Pro
	ENST00000698271.1:c.806G>C	ENST00000698271.1:p.Arg269Pro
	ENST00000698272.1:c.767G>C	ENST00000698272.1:p.Arg256Pro
	ENST00000698273.1:c.767G>C	ENST00000698273.1:p.Arg256Pro

Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics	Show details

Frequency

JP	HGVD:0.462
	ToMMo:0.440
	NCBN:[No Data.]
	NCBN(Hondo):[No Data.]
	NCBN(Ryukyu):[No Data.]
East asia	ExAC:0.431

Prediction

ClinVar

Clinical Significance	Benign
Review star
Show details

Links

TCN2

Type	Database	ID	Link
Gene	MIM	613441	OMIM
	HGNC	11653	HGNC
	Ensembl	ENSG00000185339	Ensembl
	NCBI		NCBI
	Gene Cards		Gene Cards
	OncoKB		OncoKB

Type	Database	ID	Link
Variant	TogoVar	tgv65703251	TogoVar
	COSMIC
	MONDO

Disease area statistics

[No Data.]

MGeND

[No Data.]

ClinVar

Clinical significance	Last evaluated	Review status	Condition	Origin	Links
Benign	2007-06-01	no assertion criteria provided	TRANSCOBALAMIN II POLYMORPHISM	germline	Detail
Benign	2024-02-01	criteria provided, multiple submitters, no conflicts	transcobalamin II deficiency	germline unknown	Detail
Benign	2016-03-28	criteria provided, single submitter	not specified	germline	Detail
Benign	2018-07-25	criteria provided, single submitter	not provided	germline unknown	Detail

CIViC

[No Data.]

DisGeNET

Score	Disease name	Description	Source	Pubmed	Links
<0.001	Cardiovascular Diseases	We examined five sequence variants, i.e., I23V, G94S, P259R, S348F, and R399Q, i...	BeFree	12194912	Detail
0.004	ovarian carcinoma	Using PCR-RFLP and HRM analyses, we studied the distribution of BHMT (rs3733890)...	BeFree	22183302	Detail
0.013	Malignant neoplasm of ovary	Using PCR-RFLP and HRM analyses, we studied the distribution of BHMT (rs3733890)...	BeFree	22183302	Detail
<0.001	ovarian carcinoma	Using PCR-RFLP and HRM analyses, we studied the distribution of BHMT (rs3733890)...	BeFree	22183302	Detail
0.003	Malignant neoplasm of ovary	Using PCR-RFLP and HRM analyses, we studied the distribution of BHMT (rs3733890)...	BeFree	22183302	Detail
<0.001	Homocysteinemia	Our results, if confirmed in other populations, highlight the necessity for inve...	BeFree	16820193	Detail
0.008	hyperhomocysteinemia	Our results, if confirmed in other populations, highlight the necessity for inve...	BeFree	16820193	Detail
<0.001	Glioblastoma multiforme	We investigated MTR c.2756A>G, MTHFR c.677C>T, and a third polymorphism, t...	BeFree	17119065	Detail
<0.001	Glioblastoma multiforme	We investigated MTR c.2756A>G, MTHFR c.677C>T, and a third polymorphism, t...	BeFree	17119065	Detail
0.009	glioblastoma	We investigated MTR c.2756A>G, MTHFR c.677C>T, and a third polymorphism, t...	BeFree	17119065	Detail
<0.001	glioblastoma	We investigated MTR c.2756A>G, MTHFR c.677C>T, and a third polymorphism, t...	BeFree	17119065	Detail

Annotation

Annotations

Descrption	Source	Links
NM_000355.4(TCN2):c.776G>C (p.Arg259Pro) AND TRANSCOBALAMIN II POLYMORPHISM	ClinVar	Detail
NM_000355.4(TCN2):c.776G>C (p.Arg259Pro) AND Transcobalamin II deficiency	ClinVar	Detail
NM_000355.4(TCN2):c.776G>C (p.Arg259Pro) AND not specified	ClinVar	Detail
NM_000355.4(TCN2):c.776G>C (p.Arg259Pro) AND not provided	ClinVar	Detail
We examined five sequence variants, i.e., I23V, G94S, P259R, S348F, and R399Q, in the TC gene as pos...	DisGeNET	Detail
Using PCR-RFLP and HRM analyses, we studied the distribution of BHMT (rs3733890), MTHFD1 (rs2236225)...	DisGeNET	Detail
Using PCR-RFLP and HRM analyses, we studied the distribution of BHMT (rs3733890), MTHFD1 (rs2236225)...	DisGeNET	Detail
Using PCR-RFLP and HRM analyses, we studied the distribution of BHMT (rs3733890), MTHFD1 (rs2236225)...	DisGeNET	Detail
Using PCR-RFLP and HRM analyses, we studied the distribution of BHMT (rs3733890), MTHFD1 (rs2236225)...	DisGeNET	Detail
Our results, if confirmed in other populations, highlight the necessity for investigation of the tra...	DisGeNET	Detail
Our results, if confirmed in other populations, highlight the necessity for investigation of the tra...	DisGeNET	Detail
We investigated MTR c.2756A>G, MTHFR c.677C>T, and a third polymorphism, transcobalamin 2 c.77...	DisGeNET	Detail
We investigated MTR c.2756A>G, MTHFR c.677C>T, and a third polymorphism, transcobalamin 2 c.77...	DisGeNET	Detail
We investigated MTR c.2756A>G, MTHFR c.677C>T, and a third polymorphism, transcobalamin 2 c.77...	DisGeNET	Detail
We investigated MTR c.2756A>G, MTHFR c.677C>T, and a third polymorphism, transcobalamin 2 c.77...	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: rs1801198 dbSNP
Genome: hg19
Position: chr22:31,011,610-31,011,610
Variant Type: snv
Reference Allele: G
Alternative Allele: C
Filtering Status (HGVD): PASS
# of samples (HGVD): 1210
Mean of sample read depth (HGVD): 208.60
Standard deviation of sample read depth (HGVD): 97.07
Number of reference allele (HGVD): 1302
Number of alternative allele (HGVD): 1118
Allele Frequency (HGVD): 0.46198347107438015
Gene Symbol (HGVD): TCN2
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)): rs1801198
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 0.4405
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 7382
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 16760
East Asian Chromosome Counts (ExAC): 8614
East Asian Allele Counts (ExAC): 3713
East Asian Heterozygous Counts (ExAC): 2114
East Asian Homozygous Counts (ExAC): 799
East Asian Allele Frequency (ExAC): 0.4310424889714418
Chromosome Counts in All Race (ExAC): 121212
Allele Counts in All Race (ExAC): 68766
Heterozygous Counts in All Race (ExAC): 28521
Homozygous Counts in All Race (ExAC): 20120
Allele Frequency in All Race (ExAC): 0.5673200673200673

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