Variant Details

Variant: nsv471621

Internal ID

15214440

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr3:195690793..196068603	hg38	UCSC Ensembl
Inner	chr3:195417664..195795474	hg19	UCSC Ensembl
Inner	chr3:196902845..197279871	hg18	UCSC Ensembl
Inner	chr3:196744969..197121995	hg16	UCSC Ensembl

Cytoband

3q29

Allele length

Assembly	Allele length
hg38	377811
hg19	377811
hg18	377027
hg16	377027

Variant Type

CNV gain+loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

nssv548776, nssv548775, nssv549522, nssv549516, nssv548783, nssv549520, nssv548774, nssv549524, nssv549515, nssv548778, nssv548773, nssv548784, nssv548777, nssv549521, nssv549518, nssv548781, nssv549525, nssv549519, nssv549523, nssv548772, nssv548782, nssv549517, nssv548786, nssv548785, nssv548779, nssv548780

Samples

NA10971, JK1051A, NA10469, P86GA, NA16689, NA17058, NA17015, NA15728, NA15727, NA15733, NA15726, NA15731, NA10979, NA11523, NA10976, NA10495, NA15729, NA10970

Known Genes

MIR570, MIR6829, MUC20, MUC4, SDHAP1, TFRC, TNK2

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)

nsv471621

Frequency

Sample Size	48
Observed Gain	9
Observed Loss	9
Observed Complex	0
Frequency	n/a