gnomAD reports variants with "NA" allele count and allele frequency
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15 months ago
j.lunger18 ▴ 30

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
gnomAD SNPs vcf • 337 views
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give us an example please (build/CHROM;POS)

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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?

119625175   T   C   275 rs1192393794    Missense    0.00000e+00 NA  NA  
    119625181   CA  C   278 rs1418157431    Frameshift  4.78973e-06 9.42454e-06 1   
    119625194   T   G   281 rs779360656 Missense    4.83311e-06 NA  NA  
    119625195   C   T   282 rs1165412269    STOP Gain   0.00000e+00 NA  NA  
    119625195   C   G   282 rs1165412269    Missense    4.86485e-06 9.51059e-06 1

https://gnomad.broadinstitute.org/variant/4-119625194-T-G?dataset=gnomad_r2_1

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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.

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