A curated catalogue of human genomic structural variation




Variant Details

Variant: nsv470249



Internal ID15210122
Landmark
Location Information
TypeCoordinatesAssemblyOther Links
Innerchr8:143889098..144519234hg38UCSC Ensembl
Innerchr8:144963266..145744618hg19UCSC Ensembl
Innerchr8:145035254..145715426hg18UCSC Ensembl
Cytoband8q24.3
Allele length
AssemblyAllele length
hg38630137
hg19781353
hg18680173
Variant TypeCNV loss
Copy Number
Allele State
Allele Origin
Probe Count
Validation Flag
Merged StatusM
Merged Variants
Supporting Variantsnssv546846, nssv546842, nssv546848, nssv546830, nssv546823, nssv546820, nssv546836, nssv546850, nssv546851, nssv546835, nssv546829, nssv546859, nssv546856, nssv546838, nssv546847, nssv546828, nssv546827, nssv546849, nssv546824, nssv546858, nssv546857, nssv546855, nssv546845, nssv546853, nssv546825, nssv546831, nssv546837, nssv546834, nssv546844, nssv546826, nssv546833, nssv546841, nssv546840, nssv546822, nssv546839, nssv546852
SamplesHGDP00865, HGDP00962, HGDP00288, HGDP00891, HGDP00546, HGDP00863, HGDP00298, HGDP00789, HGDP00330, HGDP00878, HGDP00302, HGDP00876, HGDP00550, HGDP00883, HGDP00954, HGDP00825, HGDP00978, HGDP00892, HGDP00874, HGDP00881, HGDP00556, HGDP00697, HGDP01061, HGDP00543, HGDP00882, HGDP00657, HGDP01060, HGDP00661
Known GenesADCK5, BOP1, CPSF1, CYC1, CYHR1, DGAT1, EXOSC4, FAM203A, FBXL6, FOXH1, GPAA1, GPT, GRINA, HSF1, KIAA1875, KIFC2, LOC100287098, LRRC14, MAF1, MFSD3, MIR1234, MIR661, MIR6846, MIR6847, MIR6848, MIR6849, MIR6893, MIR7112-2, MIR939, MROH1, OPLAH, PARP10, PLEC, PPP1R16A, RECQL4, SCRT1, SCXA, SCXB, SHARPIN, SLC39A4, SLC52A2, SPATC1, TMEM249, TONSL, VPS28
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)nsv470249
Frequency
Sample Size443
Observed Gain0
Observed Loss28
Observed Complex0
Frequencyn/a


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