chr5:131411460:T>C Detail (hg19) (CSF2)

Information

Genome

Assembly Position
hg19 chr5:131,411,460-131,411,460
hg38 chr5:132,075,767-132,075,767 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_000758.3:c.350T>C NP_000749.2:p.Ile117Thr
Ensemble ENST00000296871.4:c.350T>C ENST00000296871.4:p.Ile117Thr
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.593
ToMMo:0.592
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.602

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 138960 OMIM
HGNC 2434 HGNC
Ensembl ENSG00000164400 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv22770776 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
0.245 asthma In two large study populations of children, the German part of the International... BeFree 17362254 Detail
0.010 asthma In two large study populations of children, the German part of the International... BeFree 17362254 Detail
<0.001 Allergic disposition In two large study populations of children, the German part of the International... BeFree 17362254 Detail
0.016 asthma In two large study populations of children, the German part of the International... BeFree 17362254 Detail
<0.001 Allergic disposition In two large study populations of children, the German part of the International... BeFree 17362254 Detail
0.002 Allergic disposition In two large study populations of children, the German part of the International... BeFree 17362254 Detail
<0.001 CARCINOMA OF VULVA We also observed significantly increased risk of HPV-positive vulvar cancers ass... BeFree 26241630 Detail
<0.001 CARCINOMA OF VULVA We also observed significantly increased risk of HPV-positive vulvar cancers ass... BeFree 26241630 Detail
<0.001 Malignant neoplasm of vulva We also observed significantly increased risk of HPV-positive vulvar cancers ass... BeFree 26241630 Detail
<0.001 Malignant neoplasm of vulva We also observed significantly increased risk of HPV-positive vulvar cancers ass... BeFree 26241630 Detail
Annotation

Annotations

DescrptionSourceLinks
In two large study populations of children, the German part of the International Study of Asthma and... DisGeNET Detail
In two large study populations of children, the German part of the International Study of Asthma and... DisGeNET Detail
In two large study populations of children, the German part of the International Study of Asthma and... DisGeNET Detail
In two large study populations of children, the German part of the International Study of Asthma and... DisGeNET Detail
In two large study populations of children, the German part of the International Study of Asthma and... DisGeNET Detail
In two large study populations of children, the German part of the International Study of Asthma and... DisGeNET Detail
We also observed significantly increased risk of HPV-positive vulvar cancers associated with variant... DisGeNET Detail
We also observed significantly increased risk of HPV-positive vulvar cancers associated with variant... DisGeNET Detail
We also observed significantly increased risk of HPV-positive vulvar cancers associated with variant... DisGeNET Detail
We also observed significantly increased risk of HPV-positive vulvar cancers associated with 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
hg19
Position
chr5:131,411,460-131,411,460
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1194
Mean of sample read depth (HGVD)
87.55
Standard deviation of sample read depth (HGVD)
43.62
Number of reference allele (HGVD)
973
Number of alternative allele (HGVD)
1415
Allele Frequency (HGVD)
0.5925460636515912
Gene Symbol (HGVD)
CSF2
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))
rs25882
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.5916
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
9915
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8474
East Asian Allele Counts (ExAC)
5100
East Asian Heterozygous Counts (ExAC)
2048
East Asian Homozygous Counts (ExAC)
1526
East Asian Allele Frequency (ExAC)
0.6018409251829124
Chromosome Counts in All Race (ExAC)
119860
Allele Counts in All Race (ExAC)
31687
Heterozygous Counts in All Race (ExAC)
21997
Homozygous Counts in All Race (ExAC)
4845
Allele Frequency in All Race (ExAC)
0.264366761221425
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