A curated catalogue of human genomic structural variation




Variant Details

Variant: nssv545860



Internal ID15207861
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr9:69485135..69504046hg38UCSC Ensembl
Innerchr9:72100051..72118962hg19UCSC Ensembl
Innerchr9:71289871..71308782hg18UCSC Ensembl
Cytoband9q21.11
Allele length
AssemblyAllele length
hg3818912
hg1918912
hg1818912
Variant TypeCNV loss
Copy Number1
Allele StateHeterozygous
Allele Origin
Probe Count
Validation Flag
Merged StatusS
Merged Variantsnsv471307
Supporting Variants
SamplesHGDP00688
Known GenesAPBA1
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
Comments
ReferenceJakobsson_et_al_2008
Pubmed ID18288195
Accession Number(s)nssv545860
Frequency
Sample Size443
Observed Gain0
Observed Loss1
Observed Complex0
Frequencyn/a


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