A curated catalogue of human genomic structural variation

Variant Details

Variant: nssv545255

Internal ID15208115
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr16:1971892..2197361hg38UCSC Ensembl
Innerchr16:2021893..2247362hg19UCSC Ensembl
Innerchr16:1961894..2187363hg18UCSC Ensembl
Allele length
AssemblyAllele length
Variant TypeCNV loss
Copy Number1
Allele StateHeterozygous
Allele Origin
Probe Count
Validation Flag
Merged StatusS
Merged Variantsnsv471072
Supporting Variants
Known GenesCASKIN1, GFER, MIR1225, MIR3180-5, MIR4516, MIR6511B-1, NOXO1, NPW, NTHL1, PKD1, RAB26, SLC9A3R2, SNORD60, SYNGR3, TBL3, TRAF7, TSC2, ZNF598
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
Pubmed ID18288195
Accession Number(s)nssv545255
Sample Size443
Observed Gain0
Observed Loss1
Observed Complex0

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