Variant Details

Variant: dgv1649e212

Internal ID

20150105

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
	chr5:139514240..139534907	hg38	UCSC Ensembl
	chr5:138893825..138914492	hg19	UCSC Ensembl

Cytoband

5q31.2

Allele length

Assembly	Allele length
hg38	20668
hg19	20668

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

esv3570444, esv3570446, esv3570441, esv3570445, esv3570443

Samples

400075MR, 401366WD, 401162TM, 400926LJ, 400439IM, 400789KV, 401275SJ, 401592NR, 400906BR, 400970VE, 401911FL, 400272AE, 401783BD, 400595CP, 401918CA, 401698SB, 400625FT, 401824MM, 400277LM, 401190WC, 400379BB, 400131CM, 400674CA, 400438DB, 400588BE, 401690HA, 401832MC, 400307HW, 400121PL, 400650RM, 400385LJ, 400374LB, 401773AM, 400198MD, 401050GS, 401386WA, 400007RG, 400738WM, 402063WM, 401251WN, 400040CN, 401091HS, 400768MN, 401717LP, 401357MH, 401210PB, 400496BL, 401185LE, 400375KA, 400381CA, 400994HJ, 400076LC, 400265LK, 400124FR, 400171BJ, 400547BS, 401262RR, 401443JK, 401087SF, 400211BJ, 400978JG, 401307VR, 401700BN, 401182OC, 400430KV, 401334DH, 400156WT, 401847RK, 400295PS, 400069CN, 401288LD, 401010HT, 400267GD, 401571SD, 401149VA, 400859SC, 400586RD, 400072GR, 4000046CJ, 402008MC, 400013TA, 400209BS, 400540BM, 401490TL, 400645KM, 401180GR, 401102RD

Known Genes

Method

SNP array

Analysis

We used four separate algorithms to detect CNVs; Affymetrix Chromosome Analysis Suite (ChAS), iPattern, Nexus and Partek. Our primary analysis was performed based on ChAS CNV calls, which were then supported using the remaining three algorithms to construct a confidence set of CNVs. For all algorithms, we have used 8 probes and >1kb as a base line cutoff for CNV detection.

Platform

Affymetrix CytoScan HD 2.7M array

Comments

Reference

Uddin_et_al_2014

Pubmed ID

25503493

Accession Number(s)

dgv1649e212

Frequency

Sample Size	873
Observed Gain	0
Observed Loss	87
Observed Complex	0
Frequency	n/a