A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv433259



Internal ID15031841
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr10:46841793..46946699hg38UCSC Ensembl
Innerchr10:48792663..48897569hg19UCSC Ensembl
Innerchr10:48412669..48517575hg18UCSC Ensembl
Innerchr10:48412669..48517575hg17UCSC Ensembl
Cytoband10q11.22
Allele length
AssemblyAllele length
hg38104907
hg19104907
hg18104907
hg17104907
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv463140
SamplesNA12878
Known GenesFRMPD2P1, PTPN20A, PTPN20B
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)nsv433259
Frequency
Sample Size9
Observed Gain0
Observed Loss1
Observed Complex0
Frequencyn/a


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