A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv470051



Internal ID15209924
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr4:88723780..89721993hg38UCSC Ensembl
Innerchr4:89644931..90643144hg19UCSC Ensembl
Innerchr4:89863954..90862167hg18UCSC Ensembl
Cytoband4q22.1
Allele length
AssemblyAllele length
hg38998214
hg19998214
hg18998214
Variant TypeCNV gain
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv546334, nssv546335
SamplesHGDP00721, HGDP00351
Known GenesFAM13A, FAM13A-AS1, GPRIN3, TIGD2
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
CommentsDouble-copy duplication
ReferenceJakobsson_et_al_2008
Pubmed ID18288195
Accession Number(s)nsv470051
Frequency
Sample Size443
Observed Gain2
Observed Loss0
Observed Complex0
Frequencyn/a


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