chr22:31006860:A>G Detail (hg19) (TCN2)
Information
Genome
Assembly | Position |
---|---|
hg19 | chr22:31,006,860-31,006,860 |
hg38 | chr22:30,610,873-30,610,873 View the variant detail on this assembly version. |
HGVS
Type | Transcript | Protein |
---|---|---|
RefSeq | NM_000355.3:c.67A>G | NP_000346.2:p.Ile23Val |
NM_001184726.1:c.67A>G | NP_001171655.1:p.Ile23Val | |
Ensemble | ENST00000215838.8:c.67A>G | ENST00000215838.8:p.Ile23Val |
Summary
MGeND
Clinical significance | |
Variant entry | |
GWAS entry | |
Disease area statistics | Show details |
Frequency
JP | HGVD:0.017 |
ToMMo:0.018 | |
NCBN:[No Data.] | |
NCBN(Hondo):[No Data.] | |
NCBN(Ryukyu):[No Data.] | |
East asia | ExAC:0.021 |
Prediction
ClinVar
Clinical Significance |
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Review star | ![]() |
Show details |
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
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 |
<0.001 | Gastritis, Atrophic | A genetic variant of TCN2 (rs9606756) related to lower vitamin B12 levels was mo... | BeFree | 25681243 | Detail |
<0.001 | Anemia, Pernicious | A genetic variant of TCN2 (rs9606756) related to lower vitamin B12 levels was mo... | BeFree | 25681243 | Detail |
Annotation
Annotations
Descrption | Source | Links |
---|---|---|
NM_000355.4(TCN2):c.67A>G (p.Ile23Val) AND Transcobalamin II deficiency | ClinVar | Detail |
NM_000355.4(TCN2):c.67A>G (p.Ile23Val) 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 |
A genetic variant of TCN2 (rs9606756) related to lower vitamin B12 levels was more frequent in perni... | DisGeNET | Detail |
A genetic variant of TCN2 (rs9606756) related to lower vitamin B12 levels was more frequent in perni... | 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
- rs9606756 dbSNP
- Genome
- hg19
- Position
- chr22:31,006,860-31,006,860
- Variant Type
- snv
- Reference Allele
- A
- Alternative Allele
- G
- Filtering Status (HGVD)
- PASS
- # of samples (HGVD)
- 1199
- Mean of sample read depth (HGVD)
- 49.45
- Standard deviation of sample read depth (HGVD)
- 25.91
- Number of reference allele (HGVD)
- 2358
- Number of alternative allele (HGVD)
- 40
- Allele Frequency (HGVD)
- 0.016680567139282735
- 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))
- rs9606756
- Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 0.0175
- Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
- 293
- 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)
- 184
- East Asian Heterozygous Counts (ExAC)
- 176
- East Asian Homozygous Counts (ExAC)
- 4
- East Asian Allele Frequency (ExAC)
- 0.02127659574468085
- Chromosome Counts in All Race (ExAC)
- 121344
- Allele Counts in All Race (ExAC)
- 14139
- Heterozygous Counts in All Race (ExAC)
- 12195
- Homozygous Counts in All Race (ExAC)
- 972
- Allele Frequency in All Race (ExAC)
- 0.11651997626582279
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