A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv470114



Internal ID15209987
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr19:3372516..3855979hg38UCSC Ensembl
Innerchr19:3372514..3855977hg19UCSC Ensembl
Innerchr19:3323514..3806977hg18UCSC Ensembl
Cytoband19p13.3
Allele length
AssemblyAllele length
hg38483464
hg19483464
hg18483464
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv546443, nssv546447, nssv546444, nssv546446, nssv546445
SamplesHGDP00288, HGDP00550, HGDP00290, HGDP00556, HGDP01397
Known GenesAPBA3, C19orf71, C19orf77, CACTIN, CACTIN-AS1, DOHH, FZR1, GIPC3, HMG20B, MATK, MFSD12, MRPL54, NFIC, PIP5K1C, RAX2, TBXA2R, TJP3, ZFR2
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)nsv470114
Frequency
Sample Size443
Observed Gain0
Observed Loss5
Observed Complex0
Frequencyn/a


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