A curated catalogue of human genomic structural variation

Variant Details

Variant: nsv471011

Internal ID15210884
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr5:35860966..36003115hg38UCSC Ensembl
Innerchr5:35861068..36003217hg19UCSC Ensembl
Innerchr5:35896825..36038974hg18UCSC Ensembl
Allele length
AssemblyAllele length
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv545115
Known GenesCAPSL, IL7R, LOC100506406, UGT3A1
MethodSNP array
AnalysisWe used the previously validated default quality control criteria, excluding samples with a log R ratio standard deviation of >0.28, a median B allele frequency of >0.55 or <0.45, or a B allele frequency drift of >0.002 (for more details see Wang et al. 2007). As the PennCNV algorithm is more sensitive and specific to CNVs covering greater numbers of SNPs in the HumanHap550 array, use of a minimum number of SNPs in CNV detection increases the reliability of CNV calls (with a consequent reduction in calls per individual). We set 10 SNPs as the minimum detection threshold in the algorithm.
PlatformIllumina HumanHap550 Genotyping BeadChip v3
CommentsSingle-copy duplication
Pubmed ID18288195
Accession Number(s)nsv471011
Sample Size443
Observed Gain1
Observed Loss0
Observed Complex0

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