A curated catalogue of human genomic structural variation




Variant Details

Variant: nssv463171



Internal ID15378242
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr15:22738859..23119335hg38UCSC Ensembl
Innerchr15:22753733..23134244hg19UCSC Ensembl
Innerchr15:20305097..20685685hg18UCSC Ensembl
Innerchr15:20305097..20685685hg17UCSC Ensembl
Cytoband15q11.2
Allele length
AssemblyAllele length
hg38380477
hg19380512
hg18380589
hg17380589
Variant TypeCNV loss
Copy Number
Allele StateHemizygous
Allele Origin
Probe Count
Validation Flag
Merged StatusS
Merged Variantsnsv433290
Supporting Variants
SamplesNA18507
Known GenesCYFIP1, LOC283683, NIPA1, NIPA2, TUBGCP5
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)nssv463171
Frequency
Sample Size9
Observed Gain0
Observed Loss1
Observed Complex0
Frequencyn/a


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