chr22:30623057:G>A Detail (hg38) (TCN2)

Information

Genome

Assembly Position
hg19 chr22:31,019,044-31,019,044 View the variant detail on this assembly version.
hg38 chr22:30,623,057-30,623,057

HGVS

Type Transcript Protein
RefSeq NM_000355.3:c.1196G>A NP_000346.2:p.Arg399Gln
NM_001184726.1:c.1115G>A NP_001171655.1:p.Arg372Gln
Ensemble ENST00000215838.8:c.1196G>A ENST00000215838.8:p.Arg399Gln
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.002
ToMMo:<0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.003

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 tgv65703664 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2024-01-31 criteria provided, multiple submitters, no conflicts transcobalamin II deficiency germline Detail
Benign 2018-05-31 criteria provided, single submitter not specified unknown Detail
Benign 2019-02-08 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
Annotation

Annotations

DescrptionSourceLinks
NM_000355.4(TCN2):c.1196G>A (p.Arg399Gln) AND Transcobalamin II deficiency ClinVar Detail
NM_000355.4(TCN2):c.1196G>A (p.Arg399Gln) AND not specified ClinVar Detail
NM_000355.4(TCN2):c.1196G>A (p.Arg399Gln) 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

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
rs4820889 dbSNP
Genome
hg38
Position
chr22:30,623,057-30,623,057
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
1174
Mean of sample read depth (HGVD)
31.00
Standard deviation of sample read depth (HGVD)
24.65
Number of reference allele (HGVD)
2344
Number of alternative allele (HGVD)
4
Allele Frequency (HGVD)
0.0017035775127768314
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))
rs4820889
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0008
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
13
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)
22
East Asian Heterozygous Counts (ExAC)
22
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.002543940795559667
Chromosome Counts in All Race (ExAC)
121386
Allele Counts in All Race (ExAC)
4262
Heterozygous Counts in All Race (ExAC)
3976
Homozygous Counts in All Race (ExAC)
143
Allele Frequency in All Race (ExAC)
0.03511113307959732
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