A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2757138



Internal ID9632597
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr5:129307936..129427181hg38UCSC Ensembl
Innerchr5:128643629..128762874hg19UCSC Ensembl
Innerchr5:128671528..128790773hg18UCSC Ensembl
Innerchr5:128671528..128790773hg17UCSC Ensembl
Cytoband5q23.3
Allele length
AssemblyAllele length
hg38119246
hg19119246
hg18119246
hg17119246
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2759377
Supporting Variantsessv18870, essv21957
SamplesNA07029, NA07000
Known GenesMIR4460
MethodSNP array
AnalysisThe algorithm used to call CNVs using the 500K EA platform was developed to accurately define CNV regions using a large set of reference samples and is described in detail in a separate publication (Komura 2006). The algorithm contains three major parts: 1) Intensity pre-processing using an improved version of Genomic Imbalance Map (GIM) (Ishikawa et al. 2005), including probe selection, noise reduction, normalization, and intensity ratio adjustment based on affinity differences between alleles of a SNP, 2) CNV extraction, which identifies CNVs from all pair-wise comparisons using a modified SW-ARRAY, and 3) A copy number inference step which utilizes signal ratios and SNP information to more precisely define CNV boundaries and the copy number within each region.
PlatformAffymetrix GeneChip Early Access Mapping 500K Set Array (250K_Nsp_SNP)
Comments
ReferenceRedon_et_al_2006
Pubmed ID17122850
Accession Number(s)esv2757138
Frequency
Sample Size270
Observed Gain0
Observed Loss2
Observed Complex0
Frequencyn/a


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