A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv433359



Internal ID15031941
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr3:20049416..20546080hg38UCSC Ensembl
Innerchr3:20090908..20587572hg19UCSC Ensembl
Innerchr3:20065912..20562576hg18UCSC Ensembl
Innerchr3:20065912..20562576hg17UCSC Ensembl
Cytoband3p24.3
Allele length
AssemblyAllele length
hg38496665
hg19496665
hg18496665
hg17496665
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv463240
SamplesNA15510
Known GenesKAT2B, SGOL1, SGOL1-AS1
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)nsv433359
Frequency
Sample Size9
Observed Gain1
Observed Loss0
Observed Complex0
Frequencyn/a


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