chr4:24799693:G>A Detail (hg38) (SOD3)

Information

Genome

Assembly Position
hg19 chr4:24,801,315-24,801,315 View the variant detail on this assembly version.
hg38 chr4:24,799,693-24,799,693

HGVS

Type Transcript Protein
RefSeq NM_003102.2:c.172G>A NP_003093.2:p.Ala58Thr
Ensemble ENST00000382120.4:c.172G>A ENST00000382120.4:p.Ala58Thr
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.286
ToMMo:0.282
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.401

Prediction

ClinVar

Clinical Significance 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 tgv16416798 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2019-10-17 criteria provided, single submitter SOD3-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
<0.001 Glioma Using single-locus analysis, we identified four SNPs (SOD2 V16A, SOD3 T58A, GPX1... BeFree 23259684 Detail
<0.001 Glioma Using single-locus analysis, we identified four SNPs (SOD2 V16A, SOD3 T58A, GPX1... BeFree 23259684 Detail
<0.001 Glioma Using single-locus analysis, we identified four SNPs (SOD2 V16A, SOD3 T58A, GPX1... BeFree 23259684 Detail
<0.001 Glioma Using single-locus analysis, we identified four SNPs (SOD2 V16A, SOD3 T58A, GPX1... BeFree 23259684 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_003102.4(SOD3):c.172G>A (p.Ala58Thr) AND SOD3-related disorder ClinVar Detail
Using single-locus analysis, we identified four SNPs (SOD2 V16A, SOD3 T58A, GPX1 -46 C/T, and NOS1 3... DisGeNET Detail
Using single-locus analysis, we identified four SNPs (SOD2 V16A, SOD3 T58A, GPX1 -46 C/T, and NOS1 3... DisGeNET Detail
Using single-locus analysis, we identified four SNPs (SOD2 V16A, SOD3 T58A, GPX1 -46 C/T, and NOS1 3... DisGeNET Detail
Using single-locus analysis, we identified four SNPs (SOD2 V16A, SOD3 T58A, GPX1 -46 C/T, and NOS1 3... 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
chr4:24,799,693-24,799,693
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1163
Mean of sample read depth (HGVD)
61.02
Standard deviation of sample read depth (HGVD)
29.45
Number of reference allele (HGVD)
1660
Number of alternative allele (HGVD)
666
Allele Frequency (HGVD)
0.2863284608770421
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))
rs2536512
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.2821
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
4720
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16730
East Asian Chromosome Counts (ExAC)
3212
East Asian Allele Counts (ExAC)
1288
East Asian Heterozygous Counts (ExAC)
896
East Asian Homozygous Counts (ExAC)
196
East Asian Allele Frequency (ExAC)
0.40099626400996263
Chromosome Counts in All Race (ExAC)
56578
Allele Counts in All Race (ExAC)
34130
Heterozygous Counts in All Race (ExAC)
13826
Homozygous Counts in All Race (ExAC)
10152
Allele Frequency in All Race (ExAC)
0.6032380077061755
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