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Confusing allele notation for SNP data

I am working on some imputed data and one of the SNPs I am interested in shows up after imputation as:

name position alleles
22:39359355:C:<cn0>:39379392 39359355 C CN0

I am confused as to what C CNO means. Is this a CNV or an indel?

Thanks

snp
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written by m98 m98

Might be important to specify how you did the imputation. Try to be as informative as possible.

Anyways, given that you copied this correctly this is CN0 (zero) not CNO.

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written by WouterDeCoster WouterDeCoster

My apologies.

This SNP has indeed been imputed using Phase3 1000 Genomes data and the software IMPUTE2. To me this SNP appears to be a CNV and the nomenclature means that one allele is 0 and the other is <cn0>, whatever this means. I am just quite confused because this SNP doesn't appear to be a CNV according to dbSNP, but rather an actual single nucleotide variant. https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs=868638441

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written by m98 m98

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