chr22:30610873:A>G Detail (hg38) (TCN2)

Information

Genome

Assembly Position
hg19 chr22:31,006,860-31,006,860 View the variant detail on this assembly version.
hg38 chr22:30,610,873-30,610,873

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 Benign
Review star
Show details
Links
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 tgv65702748 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2024-02-01 criteria provided, multiple submitters, no conflicts transcobalamin II deficiency germline Detail
Benign 2018-10-17 criteria provided, single submitter not provided germline 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
<0.001 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

DescrptionSourceLinks
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
hg38
Position
chr22:30,610,873-30,610,873
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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