I have an interesting variant (very rare) found in affected and not found in unaffected and non-carriers. The variant is in a gene highly related to a very rare phenotype.
The variant is annotated by annovar as
GnomAD = 0, and ExAC = .. I looked it in ExAC , it is not found.
However when I look it up in gnomAD it is found as filtered variant as
AC0, so not high confidence genotype.
Filtered RF and AC0 Allele Count 0 Allele Number 239250 Allele Frequency 0
In my samples the variant is found with DP between 15 and 21 in my samples and all the other scores like FS and MPQ, ..etc seem okay. As follows:
GT:AD:DP:GQ:PL 0/1:7,14:21:99:383,0,13 MQ=58.73;MQRankSum=0.871;QD=13.15;ReadPosRankSum=-0.989;SOR=1.630; ABHet=0.505;ABHom=1.00;AC=1;AF=0.00;AN=2;BaseQRankSum=1.875;DP=1987;Dels=0.00;FS=3.500
Should I take the variant into account or probably assume it is an artifact. Or it could be interesting but in a hard region, so not found in ExAC At all, and found in gnomAD with low confidence? Thanks