Variant Details

Variant: nsv471189

Internal ID

15211062

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr22:25254438..25598046	hg38	UCSC Ensembl
Inner	chr22:25650405..25994013	hg19	UCSC Ensembl
Inner	chr22:23980405..24324013	hg18	UCSC Ensembl

Cytoband

22q11.23

Allele length

Assembly	Allele length
hg38	343609
hg19	343609
hg18	343609

Variant Type

CNV gain

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

nssv545525, nssv545517, nssv545534, nssv545524, nssv545522, nssv545531, nssv545535, nssv545529, nssv545538, nssv545542, nssv545540, nssv545526, nssv545539, nssv545520, nssv545541, nssv545527, nssv545518, nssv545536, nssv545533, nssv545523, nssv545528, nssv545519, nssv545530, nssv545516, nssv545537

Samples

HGDP00960, HGDP01229, HGDP00315, HGDP00698, HGDP00580, HGDP01270, HGDP01200, HGDP01257, HGDP01259, HGDP01387, HGDP01091, HGDP00938, HGDP00681, HGDP00595, HGDP01255, HGDP00880, HGDP01029, HGDP01201, HGDP00313, HGDP00453, HGDP00330

Known Genes

ADRBK2, CRYBB2P1, IGLL3P, LRP5L, MIR6817

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

Double-copy duplication

Reference

Jakobsson_et_al_2008

Pubmed ID

18288195

Accession Number(s)

nsv471189

Frequency

Sample Size	443
Observed Gain	21
Observed Loss	0
Observed Complex	0
Frequency	n/a