Variant Details

Variant: nsv470101

Internal ID

15209974

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr19:401714..1008505	hg38	UCSC Ensembl
Inner	chr19:401714..1008504	hg19	UCSC Ensembl
Inner	chr19:352714..959504	hg18	UCSC Ensembl

Cytoband

19p13.3

Allele length

Assembly	Allele length
hg38	606792
hg19	606791
hg18	606791

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

nssv546406, nssv546408, nssv546405, nssv546411, nssv546412, nssv546410, nssv546413, nssv546414, nssv546407

Samples

HGDP00315, HGDP00290, HGDP00323, HGDP00288, HGDP00298, HGDP00556, HGDP00326, HGDP00550, HGDP00302

Known Genes

ARID3A, AZU1, BSG, C2CD4C, CDC34, CFD, ELANE, FGF22, FSTL3, GRIN3B, GZMM, HCN2, KISS1R, LPPR3, MADCAM1, MED16, MIR3187, MIR4745, MISP, ODF3L2, PALM, POLRMT, PRSS57, PRTN3, PTBP1, R3HDM4, RNF126, SHC2, TPGS1, WDR18

Method

SNP array

Analysis

We 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.

Platform

Illumina HumanHap550 Genotyping BeadChip v3

Comments

Reference

Jakobsson_et_al_2008

Pubmed ID

18288195

Accession Number(s)

nsv470101

Frequency

Sample Size	443
Observed Gain	0
Observed Loss	9
Observed Complex	0
Frequency	n/a