Variant Details

Variant: nsv442962

Internal ID

15501681

Landmark

Location Information

Type	Coordinates	Assembly	Other Links
Inner	chr5:140844251..140864171	hg38	UCSC Ensembl
Inner	chr5:140223836..140243756	hg19	UCSC Ensembl
Inner	chr5:140204020..140223940	hg18	UCSC Ensembl
Inner	chr5:140204020..140223940	hg17	UCSC Ensembl

Cytoband

5q31.3

Allele length

Assembly	Allele length
hg38	19921
hg19	19921
hg18	19921
hg17	19921

Variant Type

CNV loss

Copy Number

Allele State

Allele Origin

Probe Count

Validation Flag

Merged Status

Merged Variants

Supporting Variants

nssv1629502, nssv1629507, nssv1629489, nssv1629512, nssv1629510, nssv1629503, nssv1629494, nssv1629509, nssv1629506, nssv1629495, nssv1629508, nssv1629504, nssv1629515, nssv1629492, nssv1629498, nssv1629493, nssv1629513, nssv1629500, nssv1629505, nssv1629501, nssv1629496, nssv1629491, nssv1629511, nssv1629488, nssv1629514, nssv1629497, nssv1629490, nssv1629499

Samples

NA18502, NA19141, NA18861, NA10851, NA12236, NA12801, NA18563, NA19005, NA12812, NA07019, NA19172, NA12815, NA18990, NA10855, NA07022, NA18637, NA19142, NA10830, NA12056, NA19099, NA12716, NA12057, NA19100, NA19173, NA18500, NA18609, NA07056, NA11832

Known Genes

PCDHA1, PCDHA10, PCDHA2, PCDHA3, PCDHA4, PCDHA5, PCDHA6, PCDHA7, PCDHA8, PCDHA9

Method

SNP array

Analysis

We used two computational approaches to identify CNVs: the hidden Markov model Birdseye, and an approach based on correlation between nearby probes across a population sample. To maximize the quality of reported findings, we ran duplicate experiments in independent labs, and report the CNVs that were observed in both experiments, in the same samples and at essentially identical genomic locations.

Platform

[GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array

Comments

Reference

McCarroll_et_al_2008

Pubmed ID

18776908

Accession Number(s)

nsv442962

Frequency

Sample Size	270
Observed Gain	0
Observed Loss	28
Observed Complex	0
Frequency	n/a