A curated catalogue of human genomic structural variation




Variant Details

Variant: nssv546414



Internal ID15207143
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr19:588305..844020hg38UCSC Ensembl
Innerchr19:588305..844020hg19UCSC Ensembl
Innerchr19:539305..795020hg18UCSC Ensembl
Cytoband19p13.3
Allele length
AssemblyAllele length
hg38255716
hg19255716
hg18255716
Variant TypeCNV loss
Copy Number1
Allele StateHeterozygous
Allele Origin
Probe Count
Validation Flag
Merged StatusS
Merged Variantsnsv470101
Supporting Variants
SamplesHGDP00556
Known GenesAZU1, FGF22, FSTL3, HCN2, LPPR3, MIR3187, MIR4745, MISP, PALM, POLRMT, PRSS57, PRTN3, PTBP1, RNF126
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)nssv546414
Frequency
Sample Size443
Observed Gain0
Observed Loss1
Observed Complex0
Frequencyn/a


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