A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv470247



Internal ID15210120
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr8:143283403..143615483hg38UCSC Ensembl
Innerchr8:144365573..144697653hg19UCSC Ensembl
Innerchr8:144436948..144768796hg18UCSC Ensembl
Cytoband8q24.3
Allele length
AssemblyAllele length
hg38332081
hg19332081
hg18331849
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv546818, nssv546815, nssv546816, nssv546814, nssv546808, nssv546806, nssv546817, nssv546807, nssv546812, nssv546811, nssv546813
SamplesHGDP00288, HGDP00546, HGDP00298, HGDP00302, HGDP00624, HGDP00550, HGDP00290, HGDP00978, HGDP00556, HGDP00543, HGDP00960
Known GenesEEF1D, GSDMD, MAFA, MROH6, NAPRT1, PYCRL, RHPN1, RHPN1-AS1, TIGD5, TOP1MT, TSTA3, ZC3H3, ZNF696
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)nsv470247
Frequency
Sample Size443
Observed Gain0
Observed Loss11
Observed Complex0
Frequencyn/a


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