A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv433211



Internal ID15031793
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr2:233740062..233749604hg38UCSC Ensembl
Innerchr2:234648708..234658250hg19UCSC Ensembl
Innerchr2:234313447..234322989hg18UCSC Ensembl
Innerchr2:234430708..234440250hg17UCSC Ensembl
Cytoband2q37.1
Allele length
AssemblyAllele length
hg389543
hg199543
hg189543
hg179543
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv463092
SamplesNA18517
Known GenesDNAJB3, UGT1A10, UGT1A3, UGT1A4, UGT1A5, UGT1A6, UGT1A7, UGT1A8, UGT1A9
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)nsv433211
Frequency
Sample Size9
Observed Gain0
Observed Loss1
Observed Complex0
Frequencyn/a


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