gnomAD reports variants with "NA" allele count and allele frequency
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
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give us an example please (build/CHROM;POS)
CHROM is 4. I downloaded from gnomAD exomes v2.1.1. When I searched rs779360656 in gnomAD, it shows that the allele frequency should be 0.000004518. Is it possible that I downloaded the genomes file by accident and the variants from exomes shows up?
https://gnomad.broadinstitute.org/variant/4-119625194-T-G?dataset=gnomad_r2_1
Did you ever figure this out? I have the same question.
gnomAD AF = 0 vs gnomAD AF = NA (gnomad V2)
I have proof showing its not just an error, that there is just not an entry despite it looking like there is coverage there.