chr9:32526146:G>A Detail (hg19) (RIGI, LOC130001628)

Information

Genome

Assembly Position
hg19 chr9:32,526,146-32,526,146
hg38 chr9:32,526,148-32,526,148 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_014314.3:c.19C>T NP_055129.2:p.Arg7Cys
Ensemble ENST00000379883.3:c.19C>T ENST00000379883.3:p.Arg7Cys
ENST00000679859.1:c.19C>T ENST00000679859.1:p.Arg7Cys
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.071
ToMMo:0.057
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.099

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 609631 OMIM
HGNC 19102 HGNC
Ensembl ENSG00000107201 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv36021869 TogoVar
COSMIC COSM3763882 COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2024-02-01 criteria provided, single submitter not provided germline Detail
Benign 2023-11-14 criteria provided, single submitter not specified germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.015 melanoma We investigated the association of polymorphisms in three pattern recognition re... BeFree 24621100 Detail
0.002 melanoma We investigated the association of polymorphisms in three pattern recognition re... BeFree 24621100 Detail
0.009 melanoma We investigated the association of polymorphisms in three pattern recognition re... BeFree 24621100 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_014314.4(RIGI):c.19C>T (p.Arg7Cys) AND not provided ClinVar Detail
NM_014314.4(RIGI):c.19C>T (p.Arg7Cys) AND not specified ClinVar Detail
We investigated the association of polymorphisms in three pattern recognition receptor (PRR) genes-t... DisGeNET Detail
We investigated the association of polymorphisms in three pattern recognition receptor (PRR) genes-t... DisGeNET Detail
We investigated the association of polymorphisms in three pattern recognition receptor (PRR) genes-t... 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
rs10813831 dbSNP
Genome
hg19
Position
chr9:32,526,146-32,526,146
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1141
Mean of sample read depth (HGVD)
23.91
Standard deviation of sample read depth (HGVD)
8.08
Number of reference allele (HGVD)
2121
Number of alternative allele (HGVD)
161
Allele Frequency (HGVD)
0.0705521472392638
Gene Symbol (HGVD)
DDX58
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))
rs10813831
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0572
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
958
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8368
East Asian Allele Counts (ExAC)
831
East Asian Heterozygous Counts (ExAC)
749
East Asian Homozygous Counts (ExAC)
41
East Asian Allele Frequency (ExAC)
0.09930688336520077
Chromosome Counts in All Race (ExAC)
117982
Allele Counts in All Race (ExAC)
26291
Heterozygous Counts in All Race (ExAC)
20043
Homozygous Counts in All Race (ExAC)
3124
Allele Frequency in All Race (ExAC)
0.22283907714736145
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