A curated catalogue of human genomic structural variation

Variant Details

Variant: essv9499

Internal ID9631638
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr12:323985..429872hg38UCSC Ensembl
Outerchr12:323985..434040hg38UCSC Ensembl
Innerchr12:433151..539038hg19UCSC Ensembl
Outerchr12:433151..543206hg19UCSC Ensembl
Innerchr12:303412..409299hg18UCSC Ensembl
Outerchr12:303412..413467hg18UCSC Ensembl
Innerchr12:303412..409299hg17UCSC Ensembl
Outerchr12:303412..413467hg17UCSC Ensembl
Allele length
AssemblyAllele length
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusS
Merged Variantsesv2757484
Supporting Variants
Known GenesCCDC77, KDM5A
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)
Pubmed ID17122850
Accession Number(s)essv9499
Sample Size270
Observed Gain1
Observed Loss0
Observed Complex0

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