A curated catalogue of human genomic structural variation




Variant Details

Variant: esv2758767



Internal ID9634226
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr19:51488642..52101372hg38UCSC Ensembl
Innerchr19:51991896..52604625hg19UCSC Ensembl
Innerchr19:56683708..57296437hg18UCSC Ensembl
Innerchr19:56683708..57296437hg17UCSC Ensembl
Cytoband19q13.33
Allele length
AssemblyAllele length
hg38612731
hg19612730
hg18612730
hg17612730
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsesv2758505, esv2757699, esv2757698, esv2758504
SamplesNA18621, NA19127, NA18612, NA18603, NA06993, NA10855, NA18524, NA18632, NA18854, NA12762, NA12814, NA18637, NA18537, NA18620, NA18997, NA18974, NA11832, NA18971, NA19099, NA07022
Known GenesCEACAM18, FLJ30403, FPR1, FPR2, FPR3, HAS1, HCCAT3, MIR125A, MIR99B, MIRLET7E, SIGLEC12, SIGLEC14, SIGLEC5, SIGLEC6, SPACA6P, SPACA6P-AS, ZNF175, ZNF350, ZNF432, ZNF577, ZNF613, ZNF614, ZNF615, ZNF649, ZNF841
MethodBAC aCGH
SNP array
AnalysisArray images were acquired using an Agilent laser scanner (Agilent Technologies, UK). Fluorescence intensities and log2 ratio values were extracted using Bluefuse software (Bluegnome Ltd).
The 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)
Agilent
Comments
ReferenceRedon_et_al_2006
Pubmed ID17122850
Accession Number(s)esv2758767
Frequency
Sample Size270
Observed Gain3
Observed Loss17
Observed Complex0
Frequencyn/a


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