<div dir="ltr"><div>Hi,</div><div><br></div><div>The method Bio::EnsEMBL::Variation::OverlapConsequence::rank() seems to return 'the relative rank of this OverlapConsequence when compared to other OverlapConsequence objects. This is used, for example, to determine the most severe consequence of a VariationFeature".</div>
<div><br></div><div>As shown in this example each consequence term appears to have a unique rank independently of the collective consequence terms for the input variant. Is there a dictionary somewhere of ranks and corresponding terms?</div>
<div><br></div><div><div>Location<span class="" style="white-space:pre">        </span>Allele<span class="" style="white-space:pre">    </span>Existing_variation<span class="" style="white-space:pre">        </span>SYMBOL<span class="" style="white-space:pre">    </span>SYMBOL_SOURCE<span class="" style="white-space:pre">     </span>Gene<span class="" style="white-space:pre">      </span>ENSP<span class="" style="white-space:pre">      </span>Feature<span class="" style="white-space:pre">   </span>Feature_type<span class="" style="white-space:pre">      </span>BIOTYPE<span class="" style="white-space:pre">   </span>STRAND<span class="" style="white-space:pre">    </span>CANONICAL<span class="" style="white-space:pre"> </span>EXON<span class="" style="white-space:pre">      </span>INTRON<span class="" style="white-space:pre">    </span>DISTANCE<span class="" style="white-space:pre">  </span>TSSDistance<span class="" style="white-space:pre">       </span>FeatureDistance<span class="" style="white-space:pre">   </span>Consequence<span class="" style="white-space:pre">       </span>Effect<span class="" style="white-space:pre">    </span>Rank</div>
<div>2:208228309<span class="" style="white-space:pre"> </span>T<span class="" style="white-space:pre"> </span>rs17808606<span class="" style="white-space:pre">        </span>AC007879.5<span class="" style="white-space:pre">        </span>Clone_based_vega_gene<span class="" style="white-space:pre">     </span>ENSG00000223725<span class="" style="white-space:pre">   </span>-<span class="" style="white-space:pre"> </span>ENST00000412387<span class="" style="white-space:pre">   </span>Transcript<span class="" style="white-space:pre">        </span>antisense<span class="" style="white-space:pre"> </span>-1<span class="" style="white-space:pre">        </span>-<span class="" style="white-space:pre"> </span>-<span class="" style="white-space:pre"> </span>3/4<span class="" style="white-space:pre">       </span>-<span class="" style="white-space:pre"> </span>-<span class="" style="white-space:pre"> </span>0<span class="" style="white-space:pre"> </span>intron_variant,nc_transcript_variant<span class="" style="white-space:pre">      </span>INTRONIC,WITHIN_NON_CODING_GENE<span class="" style="white-space:pre">   </span>21,23</div>
<div>2:208231478<span class="" style="white-space:pre"> </span>T<span class="" style="white-space:pre"> </span>rs17808718<span class="" style="white-space:pre">        </span>AC007879.5<span class="" style="white-space:pre">        </span>Clone_based_vega_gene<span class="" style="white-space:pre">     </span>ENSG00000223725<span class="" style="white-space:pre">   </span>-<span class="" style="white-space:pre"> </span>ENST00000412387<span class="" style="white-space:pre">   </span>Transcript<span class="" style="white-space:pre">        </span>antisense<span class="" style="white-space:pre"> </span>-1<span class="" style="white-space:pre">        </span>-<span class="" style="white-space:pre"> </span>-<span class="" style="white-space:pre"> </span>3/4<span class="" style="white-space:pre">       </span>-<span class="" style="white-space:pre"> </span>-<span class="" style="white-space:pre"> </span>0<span class="" style="white-space:pre"> </span>intron_variant,nc_transcript_variant<span class="" style="white-space:pre">      </span>INTRONIC,WITHIN_NON_CODING_GENE<span class="" style="white-space:pre">   </span>21,23</div>
<div>2:208440836<span class="" style="white-space:pre"> </span>C<span class="" style="white-space:pre"> </span>rs17811997<span class="" style="white-space:pre">        </span>CREB1<span class="" style="white-space:pre">     </span>HGNC<span class="" style="white-space:pre">      </span>ENSG00000118260<span class="" style="white-space:pre">   </span>ENSP00000412016<span class="" style="white-space:pre">   </span>ENST00000418081<span class="" style="white-space:pre">   </span>Transcript<span class="" style="white-space:pre">        </span>nonsense_mediated_decay<span class="" style="white-space:pre">   </span>1<span class="" style="white-space:pre"> </span>-<span class="" style="white-space:pre"> </span>-<span class="" style="white-space:pre"> </span>5/8<span class="" style="white-space:pre">       </span>-<span class="" style="white-space:pre"> </span>-<span class="" style="white-space:pre"> </span>0<span class="" style="white-space:pre"> </span>intron_variant,NMD_transcript_variant<span class="" style="white-space:pre">     </span>INTRONIC,NMD_TRANSCRIPT<span class="" style="white-space:pre">   </span>21,22</div>
</div><div><br></div>Thanks,<br clear="all"><div><br></div>-- <br><div dir="ltr">G.</div>
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