chr4:24801834:C>G Detail (hg19) (SOD3)

Information

Genome

Assembly Position
hg19 chr4:24,801,834-24,801,834
hg38 chr4:24,800,212-24,800,212 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_003102.2:c.691C>G NP_003093.2:p.Arg231Gly
Ensemble ENST00000382120.4:c.691C>G ENST00000382120.4:p.Arg231Gly
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.043
ToMMo:0.048
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.106

Prediction

ClinVar

Clinical Significance Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 185490 OMIM
HGNC 11181 HGNC
Ensembl ENSG00000109610 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv16416884 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Pathogenic 2004-01-06 no assertion criteria provided Superoxide dismutase, elevated extracellular germline Detail
Likely benign 2023-01-05 criteria provided, single submitter SOD3-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 pancreatic carcinoma According to the assumption that genetic variation in carcinogen metabolism furt... BeFree 20966810 Detail
0.122 pancreatic carcinoma According to the assumption that genetic variation in carcinogen metabolism furt... BeFree 20966810 Detail
0.004 Malignant neoplasm of pancreas According to the assumption that genetic variation in carcinogen metabolism furt... BeFree 20966810 Detail
<0.001 Malignant neoplasm of pancreas According to the assumption that genetic variation in carcinogen metabolism furt... BeFree 20966810 Detail
<0.001 Coronary Arteriosclerosis SOD3 R231G polymorphism associated with coronary artery disease and myocardial i... BeFree 19526392 Detail
<0.001 Coronary heart disease SOD3 R231G polymorphism associated with coronary artery disease and myocardial i... BeFree 19526392 Detail
0.007 Malignant neoplasm of lung [When numeric scores were assigned to both the SNP and demographic data, and seq... GAD 19789190 Detail
0.003 coronary artery disease SOD3 R231G polymorphism associated with coronary artery disease and myocardial i... BeFree 19526392 Detail
0.003 myocardial infarction SOD3 R231G polymorphism associated with coronary artery disease and myocardial i... BeFree 19526392 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_003102.4(SOD3):c.691C>G (p.Arg231Gly) AND Superoxide dismutase, elevated extracellular ClinVar Detail
NM_003102.4(SOD3):c.691C>G (p.Arg231Gly) AND SOD3-related disorder ClinVar Detail
According to the assumption that genetic variation in carcinogen metabolism further modifies the ris... DisGeNET Detail
According to the assumption that genetic variation in carcinogen metabolism further modifies the ris... DisGeNET Detail
According to the assumption that genetic variation in carcinogen metabolism further modifies the ris... DisGeNET Detail
According to the assumption that genetic variation in carcinogen metabolism further modifies the ris... DisGeNET Detail
SOD3 R231G polymorphism associated with coronary artery disease and myocardial infarction. The Ludwi... DisGeNET Detail
SOD3 R231G polymorphism associated with coronary artery disease and myocardial infarction. The Ludwi... DisGeNET Detail
[When numeric scores were assigned to both the SNP and demographic data, and sequentially combined b... DisGeNET Detail
SOD3 R231G polymorphism associated with coronary artery disease and myocardial infarction. The Ludwi... DisGeNET Detail
SOD3 R231G polymorphism associated with coronary artery disease and myocardial infarction. The Ludwi... 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
rs1799895 dbSNP
Genome
hg19
Position
chr4:24,801,834-24,801,834
Variant Type
snv
Reference Allele
C
Alternative Allele
G
Filtering Status (HGVD)
PASS
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
1141
Mean of sample read depth (HGVD)
108.15
Standard deviation of sample read depth (HGVD)
43.77
Number of reference allele (HGVD)
2183
Number of alternative allele (HGVD)
99
Allele Frequency (HGVD)
0.043382997370727434
Gene Symbol (HGVD)
SOD3
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))
rs1799895
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0482
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
808
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
66
East Asian Allele Counts (ExAC)
7
East Asian Heterozygous Counts (ExAC)
7
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.10606060606060606
Chromosome Counts in All Race (ExAC)
2128
Allele Counts in All Race (ExAC)
232
Heterozygous Counts in All Race (ExAC)
220
Homozygous Counts in All Race (ExAC)
6
Allele Frequency in All Race (ExAC)
0.10902255639097744
Genome browser