A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv433373



Internal ID15031955
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr5:70995423..71353594hg38UCSC Ensembl
Innerchr5:70291250..70649421hg19UCSC Ensembl
Innerchr5:70327006..70685177hg18UCSC Ensembl
Innerchr5:70327006..70685177hg17UCSC Ensembl
Cytoband5q13.2
Allele length
AssemblyAllele length
hg38358172
hg19358172
hg18358172
hg17358172
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv463254
SamplesNA18517
Known GenesGTF2H2, GTF2H2B, GTF2H2C, GTF2H2D, GUSBP9, LOC647859, NAIP
MethodSNP array
AnalysisLarge CNV discovery was accomplished by using HMMSeg, considering both the `LogR ratio' and `B-allele frequency' data for each sample simultaneously. We used a four-state model, one each for null (homozygous deletion), hemizygous deletion, diploid and amplification. Initial segmentation results were merged and filtered, requiring all variants to be larger than 1 kb in length and to span at least 10 probes for amplifications or hemizygous deletions, or 3 probes for homozygous deletions. We then used a combination of paired-end sequence maps, oligo array-CGH, and variant resequencing (described in Kidd et al. 2008) to support the calls.
PlatformIllumina Human1Mv1 DNA Analysis BeadChip (Human1Mv1_C)
Comments
ReferenceCooper_et_al_2008
Pubmed ID18776910
Accession Number(s)nsv433373
Frequency
Sample Size9
Observed Gain1
Observed Loss0
Observed Complex0
Frequencyn/a


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