Variant Details

Variant: nsv471602

Internal ID

15214421

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chrX:49205142..49320261	hg38	UCSC Ensembl
Inner	chrX:49061602..49176740	hg19	UCSC Ensembl
Inner	chrX:48948546..49063684	hg18	UCSC Ensembl
Inner	chrX:48087836..48202974	hg16	UCSC Ensembl

Cytoband

Xp11.23

Allele length

Assembly	Allele length
hg38	115120
hg19	115139
hg18	115139
hg16	115139

Variant Type

CNV gain

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

nssv550315, nssv550287, nssv550299, nssv550303, nssv550284, nssv550285, nssv550306, nssv550292, nssv550313, nssv550311, nssv550295, nssv550305, nssv550290, nssv550300, nssv550309, nssv550304, nssv550297, nssv550302, nssv550293, nssv550288, nssv550296, nssv550307, nssv550314, nssv550312, nssv550286, nssv550308, nssv550294, nssv550283, nssv550289, nssv550301, nssv550291, nssv550310, nssv550298

Samples

NA10971, NA15732, P86GA, NA16689, NA17059, NA17058, NA10473, NA10496, NA17015, NA15733, NA11521, NA15731, NA10470, NA17052, NA10979, NA11523, NA10471, NA10472, NA11776, NA10967, JK1058B, JK1061, NA10495, NA10494, NA17017, NA17051, NA15729, NA17014, NA15730, NA16688, NA10493, NA10970, NA11323

Known Genes

CACNA1F, CCDC22, FOXP3, GAGE10, PPP1R3F

Method

BAC aCGH

Analysis

Array image analysis and normalization were performed using UCSF Spot and Sproc software (Jain et al. 2002). BACs for which only one of the triplicates printed on the array yielded data, or for which the standard deviation of log2 ratio for the triplicates was 10.2, were removed from final analysis. Furthermore, we discarded BACs that failed to yield data in <20% of cases. For each hybridization experiment, we established a threshold log2 ratio of 2 SDs from the mean of all autosomal clones, and BACs that exceeded this threshold in both independent dye-swap experiments were classified as variant.

Platform

GPL4010

Comments

Reference

Sharp_et_al_2005

Pubmed ID

15918152

Accession Number(s)

nsv471602

Frequency

Sample Size	48
Observed Gain	33
Observed Loss	0
Observed Complex	0
Frequency	n/a