Variant Details

Variant: nsv438338

Internal ID

15388148

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr22:22348040..22891916	hg38	UCSC Ensembl
Inner	chr22:22702390..23234096	hg19	UCSC Ensembl
Inner	chr22:21032390..21564096	hg18	UCSC Ensembl
Inner	chr22:21026944..21558650	hg16	UCSC Ensembl

Cytoband

22q11.22

Allele length

Assembly	Allele length
hg38	543877
hg19	531707
hg18	531707
hg16	531707

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

nssv470870, nssv470846, nssv470911, nssv470868, nssv470924, nssv470864, nssv470855, nssv470917, nssv470888, nssv470871, nssv470893, nssv470873, nssv470920, nssv470884, nssv470916, nssv470901, nssv470869, nssv470862, nssv470897, nssv470854, nssv470923, nssv470925, nssv470859, nssv470894, nssv470879, nssv470891, nssv470902, nssv470926, nssv470872, nssv470853, nssv470848, nssv470849, nssv470841, nssv470910, nssv470914, nssv470921, nssv470908, nssv470886, nssv470865, nssv470876, nssv470899, nssv470883, nssv470866, nssv470919, nssv470847, nssv470845, nssv470903, nssv470898, nssv470915, nssv470850, nssv470842, nssv470895, nssv470839, nssv470913, nssv470881, nssv470922, nssv470838, nssv470860, nssv470878, nssv470880, nssv470906, nssv470875, nssv470905, nssv470900, nssv470892, nssv470912, nssv470858, nssv470889, nssv470844, nssv470882, nssv470856, nssv470927, nssv470861, nssv470843, nssv470867, nssv470890, nssv470909, nssv470887, nssv470904, nssv470877, nssv470857

Samples

NA18502, NA19203, NA19145, NA12801, NA10857, NA18526, NA07357, NA12813, NA10846, NA11992, NA07048, NA12005, NA12044, NA10855, NA10839, NA11993, NA11831, NA10831, NA19205, NA18871, NA19142, NA19154, NA12707, NA06985, NA18523, NA18945, NA18914, NA12716, NA12864, NA19140, NA12873, NA19144, NA18943, NA07055, NA06994, NA10860, NA18500, NA18972

Known Genes

GGTLC2, IGLL5, LOC648691, MIR650, POM121L1P, PRAME, ZNF280A, ZNF280B

Method

SNP array

Analysis

Hardy-Weinberg disequilibrium - we looked for genomic regions in which hetobs/hetexp consistency fell below some cutoff (we used cutoffs of 0.7 and 0.4).
Mendelian inconsistencies - for each genotype assay and population sample we defined the Mendel failure pattern of that assay as the binary vector (length 60) of Mendel consistency status across the 60 parent-offspring pair.
Null genotypes - for each genotype assay and population sample we defined the null genotype pattern of that assay as the binary vector (length 90) of null genotype calls across the 90 individuals.

Platform

Not reported

Comments

Reference

McCarroll_et_al_2006

Pubmed ID

16468122

Accession Number(s)

nsv438338

Frequency

Sample Size	269
Observed Gain	0
Observed Loss	38
Observed Complex	0
Frequency	n/a