chr12:53116149:C>T Detail (hg38) (SOAT2)

Information

Genome

Assembly Position
hg19 chr12:53,509,933-53,509,933 View the variant detail on this assembly version.
hg38 chr12:53,116,149-53,116,149

HGVS

Type Transcript Protein
RefSeq NM_003578.3:c.761C>T NP_003569.1:p.Thr254Ile
Ensemble ENST00000301466.8:c.761C>T ENST00000301466.8:p.Thr254Ile
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.395
ToMMo:0.418
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.301

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 601311 OMIM
HGNC 11178 HGNC
Ensembl ENSG00000167780 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv45923970 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 Chronic Kidney Diseases The Chi-square test, multivariable logistic regression analysis with adjustment ... BeFree 19578796 Detail
0.001 Chronic Kidney Diseases The Chi-square test, multivariable logistic regression analysis with adjustment ... BeFree 19578796 Detail
<0.001 Chronic Kidney Diseases The Chi-square test, multivariable logistic regression analysis with adjustment ... BeFree 19578796 Detail
Annotation

Annotations

DescrptionSourceLinks
The Chi-square test, multivariable logistic regression analysis with adjustment for covariates, and ... DisGeNET Detail
The Chi-square test, multivariable logistic regression analysis with adjustment for covariates, and ... DisGeNET Detail
The Chi-square test, multivariable logistic regression analysis with adjustment for covariates, and ... 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
-
Genome
hg38
Position
chr12:53,116,149-53,116,149
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1196
Mean of sample read depth (HGVD)
160.30
Standard deviation of sample read depth (HGVD)
73.69
Number of reference allele (HGVD)
1446
Number of alternative allele (HGVD)
945
Allele Frequency (HGVD)
0.39523212045169387
Gene Symbol (HGVD)
SOAT2
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))
rs2272296
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.4182
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
7009
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8632
East Asian Allele Counts (ExAC)
2599
East Asian Heterozygous Counts (ExAC)
1795
East Asian Homozygous Counts (ExAC)
402
East Asian Allele Frequency (ExAC)
0.30108897126969414
Chromosome Counts in All Race (ExAC)
121376
Allele Counts in All Race (ExAC)
23322
Heterozygous Counts in All Race (ExAC)
18124
Homozygous Counts in All Race (ExAC)
2599
Allele Frequency in All Race (ExAC)
0.19214671763775376
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