A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv471119



Internal ID15210992
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr16:89957794..90083514hg38UCSC Ensembl
Innerchr16:90024202..90149922hg19UCSC Ensembl
Innerchr16:88551703..88677423hg18UCSC Ensembl
Cytoband16q24.3
Allele length
AssemblyAllele length
hg38125721
hg19125721
hg18125721
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv545381
SamplesHGDP00460
Known GenesAFG3L1P, C16orf3, CENPBD1, DBNDD1, DEF8, GAS8, PRDM7, URAHP
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)nsv471119
Frequency
Sample Size443
Observed Gain0
Observed Loss1
Observed Complex0
Frequencyn/a


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