Why is a SNP in 23andMe data if the genotype is homozygous reference?

Question

[mprza]

Am a beginner to genomics etc, so apologies for a trivial/strange question. When looking at a 23andMe dataset, the first variant listed was the following:

rsid    chromosome  position    genotype
rs548049170 1   69869   TT

However, when I create a VCF file from this dataset, I see the following:

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  SAMPLE
1   69869   rs548049170 T   N   .   .   .   GT  0/0

Why is it considered a variant when the genotype (TT) is the same as the reference allele? Surely this isn't a variant then, so why is it included in the 23andMe data? Furthermore, everywhere that a situation like this occurs in the VCF file, the ALT column is set to N. What does this mean?

Thanks!

Answer 1

[JC]

Because you could need them for other analysis, linkage, gwas, etc