I recently downloaded sliced variant .vcf files from gnomAD. Upon downstream analysis, I noticed that some of my variants were annotated to have no reported allele count or allele frequency... Does anyone know how this could be? I assumed that if there was no count for this allele, the allele would not be in the file?
AApos <fctr> Type <fctr> change <fctr> non_cancer_AF <fctr> AF <fctr> AC <fctr> 275 Missense p.Leu275Ser 0.00000e+00 NA NA 278 Frameshift p.Lys278fs 4.78973e-06 9.42454e-06 1 281 Missense p.Phe281Leu 4.83311e-06 NA NA 282 STOP Gain p.Gln282* 0.00000e+00 NA NA 282 Missense p.Gln282Glu 4.86485e-06 9.51059e-06 1 285 Frameshift and Splice p.Lys285fs 4.86282e-06 6.56944e-05 1 291 Synonymous p.Gly291Gly 8.44602e-06 3.26648e-05 1 293 Synonymous p.Lys293Lys 4.22244e-06 2.89218e-05 1 296 Synonymous p.Val296Val 4.22215e-06 8.79678e-06 1 297 Synonymous p.Lys297Lys 1.26659e-05 2.63894e-05 3 1-10 of 28 rows