A curated catalogue of human genomic structural variation




Variant Details

Variant: nssv463111



Internal ID15031608
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr5:70995423..71080664hg38UCSC Ensembl
Innerchr5:70291250..70376491hg19UCSC Ensembl
Innerchr5:70327006..70412247hg18UCSC Ensembl
Innerchr5:70327006..70412247hg17UCSC Ensembl
Cytoband5q13.2
Allele length
AssemblyAllele length
hg3885242
hg1985242
hg1885242
hg1785242
Variant TypeCNV loss
Copy Number
Allele StateHemizygous
Allele Origin
Probe Count
Validation Flag
Merged StatusS
Merged Variantsnsv433230
Supporting Variants
SamplesNA18555
Known GenesGTF2H2, GTF2H2B, GTF2H2C, GTF2H2D, LOC647859, NAIP
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)nssv463111
Frequency
Sample Size9
Observed Gain0
Observed Loss1
Observed Complex0
Frequencyn/a


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