A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2756813



Internal ID9632272
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr16:21293950..21937801hg38UCSC Ensembl
Innerchr16:21305271..21949122hg19UCSC Ensembl
Innerchr16:21212772..21856623hg18UCSC Ensembl
Innerchr16:21212772..21856623hg17UCSC Ensembl
Cytoband16p12.1
Allele length
AssemblyAllele length
hg38643852
hg19643852
hg18643852
hg17643852
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2758636
Supporting Variantsessv2390, essv17363, essv3313
SamplesNA18976, NA18948, NA18517
Known GenesCRYM, CRYM-AS1, IGSF6, LOC100190986, LOC100271836, METTL9, NPIPB3, OTOA, RRN3P1, SLC7A5P2, SNX29P1
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)esv2756813
Frequency
Sample Size270
Observed Gain2
Observed Loss1
Observed Complex0
Frequencyn/a


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