chr12:53497402:A>G Detail (hg19) (SOAT2)

Information

Genome

Assembly Position
hg19 chr12:53,497,402-53,497,402
hg38 chr12:53,103,618-53,103,618 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_003578.3:c.41A>G NP_003569.1:p.Glu14Gly
Ensemble ENST00000301466.8:c.41A>G ENST00000301466.8:p.Glu14Gly
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.199
ToMMo:0.219
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.160

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 tgv45923423 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
0.002 Chronic Kidney Diseases Subsequent multivariable logistic regression analysis with adjustment for covari... BeFree 19282863 Detail
<0.001 Chronic Kidney Diseases Subsequent multivariable logistic regression analysis with adjustment for covari... BeFree 19282863 Detail
<0.001 Chronic Kidney Diseases Subsequent multivariable logistic regression analysis with adjustment for covari... BeFree 19282863 Detail
<0.001 Chronic Kidney Diseases Subsequent multivariable logistic regression analysis with adjustment for covari... BeFree 19282863 Detail
Annotation

Annotations

DescrptionSourceLinks
Subsequent multivariable logistic regression analysis with adjustment for covariates as well as a st... DisGeNET Detail
Subsequent multivariable logistic regression analysis with adjustment for covariates as well as a st... DisGeNET Detail
Subsequent multivariable logistic regression analysis with adjustment for covariates as well as a st... DisGeNET Detail
Subsequent multivariable logistic regression analysis with adjustment for covariates as well as a st... 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
hg19
Position
chr12:53,497,402-53,497,402
Variant Type
snv
Reference Allele
A
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1050
Mean of sample read depth (HGVD)
25.88
Standard deviation of sample read depth (HGVD)
11.35
Number of reference allele (HGVD)
1682
Number of alternative allele (HGVD)
418
Allele Frequency (HGVD)
0.19904761904761906
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))
rs9658625
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.2188
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
3666
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16756
East Asian Chromosome Counts (ExAC)
444
East Asian Allele Counts (ExAC)
71
East Asian Heterozygous Counts (ExAC)
61
East Asian Homozygous Counts (ExAC)
5
East Asian Allele Frequency (ExAC)
0.15990990990990991
Chromosome Counts in All Race (ExAC)
14124
Allele Counts in All Race (ExAC)
1629
Heterozygous Counts in All Race (ExAC)
1441
Homozygous Counts in All Race (ExAC)
94
Allele Frequency in All Race (ExAC)
0.1153355989804588
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