A curated catalogue of human genomic structural variation




Variant Details

Variant: nssv546521



Internal ID15555619
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr19:42954411..43191687hg38UCSC Ensembl
Innerchr19:43458563..43695839hg19UCSC Ensembl
Innerchr19:48150403..48387679hg18UCSC Ensembl
Cytoband19q13.31
Allele length
AssemblyAllele length
hg38237277
hg19237277
hg18237277
Variant TypeCNV gain
Copy Number3
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusS
Merged Variantsnsv470143
Supporting Variants
SamplesHGDP01029
Known GenesPSG11, PSG2, PSG5
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
CommentsSingle-copy duplication
ReferenceJakobsson_et_al_2008
Pubmed ID18288195
Accession Number(s)nssv546521
Frequency
Sample Size443
Observed Gain1
Observed Loss0
Observed Complex0
Frequencyn/a


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