A curated catalogue of human genomic structural variation

Variant Details

Variant: esv2757698

Internal ID9633157
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr19:51639378..51661874hg38UCSC Ensembl
Innerchr19:52142631..52165127hg19UCSC Ensembl
Innerchr19:56834443..56856939hg18UCSC Ensembl
Innerchr19:56834443..56856939hg17UCSC Ensembl
Allele length
AssemblyAllele length
Variant TypeCNV gain+loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsesv2758767
Supporting Variantsessv6468, essv18046, essv1559
SamplesNA06993, NA18637, NA18997
Known GenesSIGLEC14
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)esv2757698
Sample Size270
Observed Gain1
Observed Loss2
Observed Complex0

Hosted by The Centre for Applied Genomics
Grant support for DGV
Please read the usage disclaimer