A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv470687



Internal ID15210560
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr1:3356499..3763210hg38UCSC Ensembl
Innerchr1:3273063..3679774hg19UCSC Ensembl
Innerchr1:3262923..3669634hg18UCSC Ensembl
Cytoband1p36.32
Allele length
AssemblyAllele length
hg38406712
hg19406712
hg18406712
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv547675, nssv547685, nssv547677, nssv547682, nssv547680, nssv547676, nssv547684, nssv547681, nssv547674, nssv547683, nssv547686, nssv547679
SamplesHGDP00288, HGDP00546, HGDP00298, HGDP00302, HGDP00550, HGDP00825, HGDP00978, HGDP00657
Known GenesARHGEF16, CCDC27, MEGF6, MIR551A, PRDM16, TP73, TP73-AS1, TPRG1L, WRAP73
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)nsv470687
Frequency
Sample Size443
Observed Gain0
Observed Loss8
Observed Complex0
Frequencyn/a


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