A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv433378



Internal ID15031960
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr6:29886431..29905901hg38UCSC Ensembl
Innerchr6:29854208..29873678hg19UCSC Ensembl
Innerchr6:29962187..29981657hg18UCSC Ensembl
Innerchr6:29962187..29981657hg17UCSC Ensembl
Cytoband6p21.33
Allele length
AssemblyAllele length
hg3819471
hg1919471
hg1819471
hg1719471
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv463259
SamplesNA19240
Known GenesHLA-H
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)nsv433378
Frequency
Sample Size9
Observed Gain1
Observed Loss0
Observed Complex0
Frequencyn/a


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