chr3:47418189:C>T Detail (hg38) (SCAP)

Information

Genome

Assembly Position
hg19 chr3:47,459,679-47,459,679 View the variant detail on this assembly version.
hg38 chr3:47,418,189-47,418,189

HGVS

Type Transcript Protein
RefSeq NM_001320044.1:c.2392G>A NP_001306973.1:p.Val798Ile
NM_012235.3:c.2392G>A NP_036367.2:p.Val798Ile
Ensemble ENST00000265565.10:c.2392G>A ENST00000265565.10:p.Val798Ile
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.526
ToMMo:0.524
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.626

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 601510 OMIM
HGNC 30634 HGNC
Ensembl ENSG00000114650 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv12336089 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 19424605 Detail
<0.001 Chronic Kidney Diseases The Chi-square test, multivariable logistic regression analysis with adjustment ... BeFree 19424605 Detail
<0.001 Chronic Kidney Diseases The Chi-square test, multivariable logistic regression analysis with adjustment ... BeFree 19424605 Detail
0.002 Chronic Kidney Diseases The Chi-square test, multivariable logistic regression analysis with adjustment ... BeFree 19424605 Detail
0.002 Chronic Kidney Diseases The Chi-square test, multivariable logistic regression analysis with adjustment ... BeFree 19424605 Detail
0.003 myocardial infarction SREBF-2 1784G &gt; C single nucleotide polymorphism (SNP, rs2228314) and SCAP 23... BeFree 20111910 Detail
Annotation

Annotations

DescrptionSourceLinks
The Chi-square test, multivariable logistic regression analysis with adjustment for covariates, as w... DisGeNET Detail
The Chi-square test, multivariable logistic regression analysis with adjustment for covariates, as w... DisGeNET Detail
The Chi-square test, multivariable logistic regression analysis with adjustment for covariates, as w... DisGeNET Detail
The Chi-square test, multivariable logistic regression analysis with adjustment for covariates, as w... DisGeNET Detail
The Chi-square test, multivariable logistic regression analysis with adjustment for covariates, as w... DisGeNET Detail
SREBF-2 1784G &gt; C single nucleotide polymorphism (SNP, rs2228314) and SCAP 2386A &gt; G variant (... 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
chr3:47,418,189-47,418,189
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1198
Mean of sample read depth (HGVD)
62.39
Standard deviation of sample read depth (HGVD)
31.36
Number of reference allele (HGVD)
1136
Number of alternative allele (HGVD)
1260
Allele Frequency (HGVD)
0.5258764607679466
Gene Symbol (HGVD)
SCAP
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))
rs12487736
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.5241
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
8771
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16736
East Asian Chromosome Counts (ExAC)
3382
East Asian Allele Counts (ExAC)
2118
East Asian Heterozygous Counts (ExAC)
992
East Asian Homozygous Counts (ExAC)
563
East Asian Allele Frequency (ExAC)
0.6262566528681254
Chromosome Counts in All Race (ExAC)
50092
Allele Counts in All Race (ExAC)
31529
Heterozygous Counts in All Race (ExAC)
13493
Homozygous Counts in All Race (ExAC)
9018
Allele Frequency in All Race (ExAC)
0.629421863770662
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