1)For data derived from RNA sequencing and aligned to the genomic reference sequence, application of 3’HGVS rule might lead to shifting of exonic variants to the intron. For example, if the RNA seq alignment calls out deletion of last G at the exon intron junction, then application of 3' rule would shift the variant to the next intron as shown in below image. As processed mRNAs are devoid of introns, this might be a non plausible scenario. Should the 3' rule be applied in this case? How should such variants be reported? as a c. or an r.? As the RNAseq process involves conversion to cDNA and alignemnt to genomic reference, is reporting a variant as r. correct? When should the r. nomenclature be followed? Can someone please explain with an example.
