chr3:46373456:GTCAGTATCAATTCTGGAAGAATTTCCAGACA> Detail (hg38) (CCR5, CCR5AS)

Information

Genome

Assembly Position
hg19 chr3:46,414,947-46,414,978 
hg38 chr3:46,373,456-46,373,487

HGVS

Type Transcript Protein
RefSeq NM_000579.3:c.554_585delGTCAGTATCAATTCTGGAAGAATTTCCAGACA NP_000570.1:p.Ser185IlefsTer32
NM_001100168.1:c.554_585delGTCAGTATCAATTCTGGAAGAATTTCCAGACA NP_001093638.1:p.Ser185IlefsTer32
Ensemble ENST00000292303.5:c.554_585delGTCAGTATCAATTCTGGAAGAATTTCCAGACA ENST00000292303.5:p.Ser185IlefsTer32
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:<0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:<0.001

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 601373 OMIM
HGNC 1606 HGNC
Ensembl ENSG00000160791 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv12302567 TogoVar
COSMIC COSM1423390 COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
protective 2008-12-01 no assertion criteria provided Susceptibility to HIV infection germline Detail
risk factor 2008-12-01 no assertion criteria provided West Nile virus, susceptibility to germline Detail
protective 2008-12-01 no assertion criteria provided Resistance to hepatitis C virus germline Detail
risk factor 2008-12-01 no assertion criteria provided Multiple sclerosis modifier of disease progression germline Detail
Benign 2019-11-22 criteria provided, single submitter not provided germline Detail
Benign 2019-05-10 criteria provided, single submitter CCR5-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.001 vascular disease occlusive All subjects were genotyped for 13 polymorphic variants in the genes of xenobiot... BeFree 23107763 Detail
0.337 hyperhomocysteinemia All subjects were genotyped for 13 polymorphic variants in the genes of xenobiot... BeFree 23107763 Detail
<0.001 hyperhomocysteinemia All subjects were genotyped for 13 polymorphic variants in the genes of xenobiot... BeFree 23107763 Detail
0.146 Homocysteinemia All subjects were genotyped for 13 polymorphic variants in the genes of xenobiot... BeFree 23107763 Detail
<0.001 Homocysteinemia All subjects were genotyped for 13 polymorphic variants in the genes of xenobiot... BeFree 23107763 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_001394783.1(CCR5):c.554_585del (p.Ser185fs) AND Susceptibility to HIV infection ClinVar Detail
NM_001394783.1(CCR5):c.554_585del (p.Ser185fs) AND West Nile virus, susceptibility to ClinVar Detail
NM_001394783.1(CCR5):c.554_585del (p.Ser185fs) AND Resistance to hepatitis C virus ClinVar Detail
NM_001394783.1(CCR5):c.554_585del (p.Ser185fs) AND Multiple sclerosis modifier of disease progressio... ClinVar Detail
NM_001394783.1(CCR5):c.554_585del (p.Ser185fs) AND not provided ClinVar Detail
NM_001394783.1(CCR5):c.554_585del (p.Ser185fs) AND CCR5-related disorder ClinVar Detail
All subjects were genotyped for 13 polymorphic variants in the genes of xenobiotics detoxification C... DisGeNET Detail
All subjects were genotyped for 13 polymorphic variants in the genes of xenobiotics detoxification C... DisGeNET Detail
All subjects were genotyped for 13 polymorphic variants in the genes of xenobiotics detoxification C... DisGeNET Detail
All subjects were genotyped for 13 polymorphic variants in the genes of xenobiotics detoxification C... DisGeNET Detail
All subjects were genotyped for 13 polymorphic variants in the genes of xenobiotics detoxification C... 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
rs333 dbSNP
Genome
hg38
Position
chr3:46,373,456-46,373,487
Variant Type
snv
Reference Allele
GTCAGTATCAATTCTGGAAGAATTTCCAGACA
Alternative Allele
-
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))
rs333
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0001
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
2
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8652
East Asian Allele Counts (ExAC)
2
East Asian Heterozygous Counts (ExAC)
2
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
2.311604253351826E-4
Chromosome Counts in All Race (ExAC)
121234
Allele Counts in All Race (ExAC)
8805
Heterozygous Counts in All Race (ExAC)
8005
Homozygous Counts in All Race (ExAC)
400
Allele Frequency in All Race (ExAC)
0.07262814062061798
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