A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv470145



Internal ID15556704
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr19:42817913..43335936hg38UCSC Ensembl
Innerchr19:43322065..43840088hg19UCSC Ensembl
Innerchr19:48013905..48531928hg18UCSC Ensembl
Cytoband19q13.2
Allele length
AssemblyAllele length
hg38518024
hg19518024
hg18518024
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv546552, nssv546532, nssv546528, nssv546526, nssv546550, nssv546533, nssv546545, nssv546556, nssv546551, nssv546549, nssv546525, nssv546529, nssv546535, nssv546546, nssv546548, nssv546530, nssv546554, nssv546544, nssv546539, nssv546524, nssv546527, nssv546541, nssv546540, nssv546543, nssv546534, nssv546523, nssv546538, nssv546537, nssv546555, nssv546547, nssv546536
SamplesHGDP00960, HGDP01284, HGDP00678, HGDP00713, HGDP00323, HGDP00461, HGDP00934, HGDP01254, HGDP00698, HGDP00933, HGDP00346, HGDP01224, HGDP00057, HGDP01365, HGDP00582, HGDP01259, HGDP01264, HGDP00720, HGDP01397, HGDP00681, HGDP00388, HGDP00905, HGDP01318, HGDP00620, HGDP01358, HGDP01323, HGDP01186, HGDP00924, HGDP01366, HGDP01282, HGDP00330
Known GenesLOC100289650, LOC284344, PSG1, PSG10P, PSG11, PSG2, PSG4, PSG5, PSG6, PSG7, PSG9
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)nsv470145
Frequency
Sample Size443
Observed Gain0
Observed Loss31
Observed Complex0
Frequencyn/a


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