A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv471287



Internal ID15211160
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr9:17165700..17708816hg38UCSC Ensembl
Innerchr9:17165698..17708814hg19UCSC Ensembl
Innerchr9:17155698..17698814hg18UCSC Ensembl
Cytoband9p22.2
Allele length
AssemblyAllele length
hg38543117
hg19543117
hg18543117
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv545834, nssv545835
SamplesHGDP00617, HGDP00635
Known GenesCNTLN, SH3GL2
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
ReferenceJakobsson_et_al_2008
Pubmed ID18288195
Accession Number(s)nsv471287
Frequency
Sample Size443
Observed Gain2
Observed Loss0
Observed Complex0
Frequencyn/a


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