chr4:73998280:T>C Detail (hg38) (CXCL5)

Information

Genome

Assembly Position
hg19 chr4:74,863,997-74,863,997 View the variant detail on this assembly version.
hg38 chr4:73,998,280-73,998,280

HGVS

Type Transcript Protein
RefSeq NM_002994.4:c.168A>G NP_002985.1:p.Gln56=
Ensemble ENST00000296027.5:c.168A>G ENST00000296027.5:p.Gln56=
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.973
ToMMo:0.981
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.967

Prediction

ClinVar

Clinical Significance
Review star [No Data.]
Show details
Links
Type Database ID Link
Gene MIM 600324 OMIM
HGNC 10642 HGNC
Ensembl ENSG00000163735 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv17481174 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
0.070 Malignant neoplasm of breast Among premenopausal AA women, comparing variant allele carriers to non-carriers,... BeFree 23991131 Detail
<0.001 Malignant neoplasm of breast Among premenopausal AA women, comparing variant allele carriers to non-carriers,... BeFree 23991131 Detail
0.028 breast carcinoma Among premenopausal AA women, comparing variant allele carriers to non-carriers,... BeFree 23991131 Detail
0.001 breast carcinoma Among premenopausal AA women, comparing variant allele carriers to non-carriers,... BeFree 23991131 Detail
<0.001 breast carcinoma Among premenopausal AA women, comparing variant allele carriers to non-carriers,... BeFree 23991131 Detail
<0.001 Malignant neoplasm of breast Among premenopausal AA women, comparing variant allele carriers to non-carriers,... BeFree 23991131 Detail
Annotation

Annotations

DescrptionSourceLinks
Among premenopausal AA women, comparing variant allele carriers to non-carriers, reduced breast canc... DisGeNET Detail
Among premenopausal AA women, comparing variant allele carriers to non-carriers, reduced breast canc... DisGeNET Detail
Among premenopausal AA women, comparing variant allele carriers to non-carriers, reduced breast canc... DisGeNET Detail
Among premenopausal AA women, comparing variant allele carriers to non-carriers, reduced breast canc... DisGeNET Detail
Among premenopausal AA women, comparing variant allele carriers to non-carriers, reduced breast canc... DisGeNET Detail
Among premenopausal AA women, comparing variant allele carriers to non-carriers, reduced breast canc... 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
chr4:73,998,280-73,998,280
Variant Type
snv
Reference Allele
T
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
171.25
Standard deviation of sample read depth (HGVD)
78.17
Number of reference allele (HGVD)
65
Number of alternative allele (HGVD)
2342
Allele Frequency (HGVD)
0.9729954299958454
Gene Symbol (HGVD)
CXCL5
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))
rs425535
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.9808
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16439
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8654
East Asian Allele Counts (ExAC)
8369
East Asian Heterozygous Counts (ExAC)
275
East Asian Homozygous Counts (ExAC)
4047
East Asian Allele Frequency (ExAC)
0.9670672521377398
Chromosome Counts in All Race (ExAC)
121394
Allele Counts in All Race (ExAC)
105535
Heterozygous Counts in All Race (ExAC)
12715
Homozygous Counts in All Race (ExAC)
46410
Allele Frequency in All Race (ExAC)
0.8693592764057532
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