diff --git a/utilities/deps/small-files/annotation_criteria.tsv b/utilities/deps/small-files/annotation_criteria.tsv index 71d640dd..26e6d79a 100644 --- a/utilities/deps/small-files/annotation_criteria.tsv +++ b/utilities/deps/small-files/annotation_criteria.tsv @@ -1,13 +1,16 @@ gene_name transcript_id consequence start end frame annotation NPM1 ENST00000296930.10 frameshift_variant 860 875 1 pathogenic +NPM1 ENST00000296930.10 discard FLT3 ENST00000241453.12 missense_variant 2491 2526 likely pathogenic (FLT3-TKD) FLT3 ENST00000241453.12 inframe_insertion 2491 2526 likely pathogenic (FLT3-TKD) FLT3 ENST00000241453.12 inframe_deletion 2491 2526 likely pathogenic (FLT3-TKD) FLT3 ENST00000241453.12 inframe_insertion 1705 1942 likely pathogenic (FLT3-ITD) +FLT3 ENST00000241453.12 discard CEBPA ENST00000498907.3 inframe_deletion 814 1077 pathogenic (bZIP inframe) CEBPA ENST00000498907.3 inframe_insertion 814 1077 pathogenic (bZIP inframe) ASXL1 ENST00000375687.10 stop_gained 1720 4626 pathogenic ASXL1 ENST00000375687.10 frameshift_variant 1720 4626 pathogenic +ASXL1 ENST00000375687.10 discard BCOR ENST00000378444.9 frameshift_variant pathogenic BCOR ENST00000378444.9 stop_gained pathogenic BCOR ENST00000378444.9 stop_lost pathogenic @@ -23,7 +26,7 @@ EZH2 ENST00000320356.7 inframe_insertion 1507 1851 possible pathogenic (CXC) EZH2 ENST00000320356.7 missense_variant 1852 2253 possible pathogenic (SET) EZH2 ENST00000320356.7 inframe_deletion 1852 2253 possible pathogenic (SET) EZH2 ENST00000320356.7 inframe_insertion 1852 2253 possible pathogenic (SET) -EZH2 ENST00000320356.7 frameshift pathogenic +EZH2 ENST00000320356.7 frameshift_variant pathogenic EZH2 ENST00000320356.7 stop_gained pathogenic EZH2 ENST00000320356.7 stop_lost pathogenic RUNX1 ENST00000675419.1 frameshift_variant pathogenic @@ -45,6 +48,7 @@ SF3B1 ENST00000335508.11 stop_lost discard SRSF2 ENST00000359995.10 missense_variant 283 284 pathogenic SRSF2 ENST00000359995.10 inframe_insertion 283 284 pathogenic SRSF2 ENST00000359995.10 inframe_deletion 283 284 pathogenic +SRSF2 ENST00000359995.10 discard STAG2 ENST00000371145.8 frameshift_variant pathogenic STAG2 ENST00000371145.8 start_lost pathogenic STAG2 ENST00000371145.8 stop_gained pathogenic @@ -57,6 +61,7 @@ U2AF1 ENST00000291552.9 inframe_deletion 100 105 possible pathogenic U2AF1 ENST00000291552.9 missense_variant 466 477 possible pathogenic U2AF1 ENST00000291552.9 inframe_insertion 466 477 possible pathogenic U2AF1 ENST00000291552.9 inframe_deletion 466 477 possible pathogenic +U2AF1 ENST00000291552.9 discard ZRSR2 ENST00000307771.8 frameshift_variant pathogenic ZRSR2 ENST00000307771.8 start_lost pathogenic ZRSR2 ENST00000307771.8 stop_gained pathogenic @@ -68,7 +73,7 @@ TP53 ENST00000269305.9 start_lost pathogenic TP53 ENST00000269305.9 stop_gained pathogenic TP53 ENST00000269305.9 stop_lost pathogenic TP53 ENST00000269305.9 missense_variant 742 744 pathogenic -TP53 ENST00000269305.9 missense possible pathogenic +TP53 ENST00000269305.9 missense_variant possible pathogenic TP53 ENST00000269305.9 inframe_insertion possible pathogenic TP53 ENST00000269305.9 inframe_deletion possible pathogenic TP53g ENST00000455263.6 994-2 *2 possible pathogenic (alt exon 10 gamma) @@ -99,20 +104,23 @@ KIT ENST00000288135.6 stop_lost discard BRAF ENST00000646891.2 missense_variant 1768 1845 possible pathogenic BRAF ENST00000646891.2 inframe_deletion 1768 1845 possible pathogenic BRAF ENST00000646891.2 inframe_insertion 1768 1845 possible pathogenic +BRAF ENST00000646891.2 discard CALR ENST00000316448.10 frameshift_variant 1090 1110 2 pathogenic (type-1 (like) CALR ENST00000316448.10 frameshift_variant 1141 1251 2 pathogenic (type-2 (like) CALR ENST00000316448.10 frameshift_variant 1111 1140 2 pathogenic (other) +CALR ENST00000316448.10 discard CBL ENST00000264033.6 1096-2 1431+2 possible pathogenic (RING fingers) CSF3R ENST00000373103.5 frameshift_variant 2041 2592 pathogenic (exon 17 truncating) CSF3R ENST00000373103.5 stop_gained 2041 2592 pathogenic (exon 17 truncating) CSF3R ENST00000373103.5 stop_lost 2041 2592 pathogenic (exon 17 truncating) CSF3R ENST00000373103.5 missense_variant 1724 1864 possible pahtogenic (exon 14 activating) CSF3R ENST00000373103.5 1724 1864 possible pathogenic +CSF3R ENST00000373103.5 discard DNMT3A ENST00000321117.10 missense_variant 2644 2645 pathogenic DNMT3A ENST00000321117.10 missense_variant possible pathogenic DNMT3A ENST00000321117.10 inframe_deletion possible pathogenic DNMT3A ENST00000321117.10 inframe_insertion possible pathogenic -DNMT3A ENST00000321117.10 frameshift possible pathogenic +DNMT3A ENST00000321117.10 frameshift_variant possible pathogenic DNMT3A ENST00000321117.10 stop_gained possible pathogenic DNMT3A ENST00000321117.10 stop_lost possible pathogenic ETNK1 ENST00000671733.1 missense_variant 727 734 (only known pathogenic) @@ -162,12 +170,13 @@ PTPN11 ENST00000351677.7 frameshift_variant discard PTPN11 ENST00000351677.7 stop_gained discard PTPN11 ENST00000351677.7 stop_lost discard SETBP1 ENST00000649279.2 missense_variant 2548 2730 possible pathogenic +SETBP1 ENST00000649279.2 discard TET2 ENST00000380013.9 frameshift_variant pathogenic TET2 ENST00000380013.9 start_lost pathogenic TET2 ENST00000380013.9 stop_gained pathogenic TET2 ENST00000380013.9 start_lost pathogenic -TET2 ENST00000380013.9 missense_variant 3310 4443 possible pathogenic (Cat. Dom) -TET2 ENST00000380013.9 missense_variant 5527 6009 possible pathogenic (Cat. Dom) +TET2 ENST00000380013.9 missense_variant 3310 4443 possible pathogenic (cat. dom) +TET2 ENST00000380013.9 missense_variant 5527 6009 possible pathogenic (cat. dom) UBA1 ENST00000335972.11 discard (only known pathogenic) WT1 ENST00000452863.10 frameshift_variant 1114 1264 pathogenic WT1 ENST00000452863.10 start_lost 1114 1264 pathogenic @@ -180,4 +189,4 @@ GNB1 ENST00000378609.9 possible pathogenic MYC ENST00000621592.8 175 240 possible pathogenic (MYC box 1) NF1 ENST00000358273.9 possible pathogenic PRPF8 ENST00000304992.11 possible pathogenic -RAD21 ENST00000297338.7 possible pathogenic +RAD21 ENST00000297338.7 possible pathogenic \ No newline at end of file