A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv470107



Internal ID15209980
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr19:1782799..2100347hg38UCSC Ensembl
Innerchr19:1782798..2100346hg19UCSC Ensembl
Innerchr19:1733798..2051346hg18UCSC Ensembl
Cytoband19p13.3
Allele length
AssemblyAllele length
hg38317549
hg19317549
hg18317549
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv546434, nssv546428, nssv546429, nssv546436, nssv546432, nssv546430, nssv546433, nssv546435
SamplesHGDP00313, HGDP00298, HGDP00789, HGDP00330, HGDP00315, HGDP01397, HGDP00657
Known GenesABHD17A, ADAT3, ATP8B3, BTBD2, CSNK1G2, CSNK1G2-AS1, IZUMO4, KLF16, LOC100288123, MIR1909, MKNK2, MOB3A, REXO1, SCAMP4
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)nsv470107
Frequency
Sample Size443
Observed Gain0
Observed Loss7
Observed Complex0
Frequencyn/a


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