A curated catalogue of human genomic structural variation

Variant Details

Variant: nsv469998

Internal ID15209871
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr4:815805..1093743hg38UCSC Ensembl
Innerchr4:809593..1087531hg19UCSC Ensembl
Innerchr4:799593..1077531hg18UCSC Ensembl
Allele length
AssemblyAllele length
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv546238, nssv546236, nssv546237, nssv546234, nssv546232, nssv546233, nssv546239, nssv546235
SamplesHGDP00288, HGDP00298, HGDP00550, HGDP00290, HGDP00825, HGDP00978, HGDP00543, HGDP00661
Known GenesCPLX1, DGKQ, FGFRL1, GAK, IDUA, RNF212, SLC26A1, TMEM175
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
Pubmed ID18288195
Accession Number(s)nsv469998
Sample Size443
Observed Gain0
Observed Loss8
Observed Complex0

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