A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv433346



Internal ID15031928
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr1:629097..770988hg38UCSC Ensembl
Innerchr1:564477..706368hg19UCSC Ensembl
Innerchr1:554340..696231hg18UCSC Ensembl
Innerchr1:604340..746231hg17UCSC Ensembl
Cytoband1p36.33
Allele length
AssemblyAllele length
hg38141892
hg19141892
hg18141892
hg17141892
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variantsdgv2n14
Supporting Variantsnssv463227
SamplesNA12156
Known GenesLOC100133331, LOC100288069, MIR6723, OR4F16, OR4F29, OR4F3
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)nsv433346
Frequency
Sample Size9
Observed Gain1
Observed Loss0
Observed Complex0
Frequencyn/a


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