A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv433358



Internal ID15031940
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr3:19505692..19955016hg38UCSC Ensembl
Innerchr3:19547184..19996508hg19UCSC Ensembl
Innerchr3:19522188..19971512hg18UCSC Ensembl
Innerchr3:19522188..19971512hg17UCSC Ensembl
Cytoband3p24.3
Allele length
AssemblyAllele length
hg38449325
hg19449325
hg18449325
hg17449325
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv463239
SamplesNA15510
Known GenesEFHB, KCNH8, RAB5A
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)nsv433358
Frequency
Sample Size9
Observed Gain1
Observed Loss0
Observed Complex0
Frequencyn/a


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