diff --git a/docs/source/snv-indels.rst b/docs/source/snv-indels.rst index 74b8d152..98f695ed 100644 --- a/docs/source/snv-indels.rst +++ b/docs/source/snv-indels.rst @@ -44,8 +44,8 @@ By default, HAMLET comes with variant filters and annotations which are tuned to * - Possible pathogenic - This variant should **not** be considered pathogenic, unless there is additional evidence (*e.g.* it is a known pathogenic variant) - * - Discard - - This variant should not be considere pathogenic + * - Likely benign + - This variant should not be considered pathogenic * - Artifact - This variant is most likely an artifact produced by the pipeline, *i.e.* the variant is not truly present in the sample diff --git a/utilities/deps/small-files/annotation_criteria.tsv b/utilities/deps/small-files/annotation_criteria.tsv index 26e6d79a..2d56ddbf 100644 --- a/utilities/deps/small-files/annotation_criteria.tsv +++ b/utilities/deps/small-files/annotation_criteria.tsv @@ -1,73 +1,91 @@ gene_name transcript_id consequence start end frame annotation NPM1 ENST00000296930.10 frameshift_variant 860 875 1 pathogenic -NPM1 ENST00000296930.10 discard +NPM1 ENST00000296930.10 likely benign 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 protein_altering_variant 2491 2526 likely pathogenic (FLT3-TKD) FLT3 ENST00000241453.12 inframe_insertion 1705 1942 likely pathogenic (FLT3-ITD) -FLT3 ENST00000241453.12 discard +FLT3 ENST00000241453.12 likely benign CEBPA ENST00000498907.3 inframe_deletion 814 1077 pathogenic (bZIP inframe) CEBPA ENST00000498907.3 inframe_insertion 814 1077 pathogenic (bZIP inframe) +CEBPA ENST00000498907.3 protein_altering_variant 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 +ASXL1 ENST00000375687.10 likely benign BCOR ENST00000378444.9 frameshift_variant pathogenic BCOR ENST00000378444.9 stop_gained pathogenic BCOR ENST00000378444.9 stop_lost pathogenic +BCOR ENST00000378444.9 missense_variant possible pathogenic +BCOR ENST00000378444.9 inframe_deletion possible pathogenic +BCOR ENST00000378444.9 inframe_insertion possible pathogenic +BCOR ENST00000378444.9 protein_altering_variant possible pathogenic +EZH2 ENST00000320356.7 frameshift_variant pathogenic +EZH2 ENST00000320356.7 stop_gained pathogenic +EZH2 ENST00000320356.7 stop_lost pathogenic EZH2 ENST00000320356.7 missense_variant 280 477 possible pathogenic (D1) EZH2 ENST00000320356.7 inframe_deletion 280 477 possible pathogenic (D1) EZH2 ENST00000320356.7 inframe_insertion 280 477 possible pathogenic (D1) +EZH2 ENST00000320356.7 protein_altering_variant 280 477 possible pathogenic (D1) EZH2 ENST00000320356.7 missense_variant 652 999 possible pathogenic (D2) EZH2 ENST00000320356.7 inframe_deletion 652 999 possible pathogenic (D2) EZH2 ENST00000320356.7 inframe_insertion 652 999 possible pathogenic (D2) +EZH2 ENST00000320356.7 protein_altering_variant 652 999 possible pathogenic (D2) EZH2 ENST00000320356.7 missense_variant 1507 1851 possible pathogenic (CXC) EZH2 ENST00000320356.7 inframe_deletion 1507 1851 possible pathogenic (CXC) EZH2 ENST00000320356.7 inframe_insertion 1507 1851 possible pathogenic (CXC) +EZH2 ENST00000320356.7 protein_altering_variant 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_variant pathogenic -EZH2 ENST00000320356.7 stop_gained pathogenic -EZH2 ENST00000320356.7 stop_lost pathogenic +EZH2 ENST00000320356.7 protein_altering_variant 1852 2253 possible pathogenic (SET) +EZH2 ENST00000320356.7 possible pathogenic RUNX1 ENST00000675419.1 frameshift_variant pathogenic RUNX1 ENST00000675419.1 start_lost pathogenic RUNX1 ENST00000675419.1 stop_gained pathogenic RUNX1 ENST00000675419.1 stop_lost pathogenic -RUNX1 ENST00000675419.1 splice_acceptor_variant pathogenic -RUNX1 ENST00000675419.1 splice_donor_variant pathogenic RUNX1 ENST00000675419.1 missense_variant 230 613 possible pathogenic (RUNT) RUNX1 ENST00000675419.1 inframe_insertion 230 613 possible pathogenic (RUNT) RUNX1 ENST00000675419.1 inframe_deletion 230 613 possible pathogenic (RUNT) -RUNX1b ENST00000344691.8 533-2 724+2 possible pathogenic (alt exon 4) +RUNX1 ENST00000675419.1 protein_altering_variant 230 613 possible pathogenic (RUNT) +RUNX1 ENST00000675419.1 possible pathogenic +RUNX1b ENST00000344691.8 -2 270+2 possible pathogenic (alt exon 4) +SF3B1 ENST00000335508.11 missense_variant 1864 1869 pathogenic +SF3B1 ENST00000335508.11 missense_variant 1873 1878 pathogenic +SF3B1 ENST00000335508.11 missense_variant 1984 1986 pathogenic +SF3B1 ENST00000335508.11 missense_variant 1996 1998 pathogenic SF3B1 ENST00000335508.11 missense_variant 1720 2370 possible pathogenic (HEAT) SF3B1 ENST00000335508.11 inframe_insertion 1720 2370 possible pathogenic (HEAT) SF3B1 ENST00000335508.11 inframe_deletion 1720 2370 possible pathogenic (HEAT) -SF3B1 ENST00000335508.11 frameshift_variant discard -SF3B1 ENST00000335508.11 stop_gained discard -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 +SF3B1 ENST00000335508.11 protein_altering_variant 1720 2370 possible pathogenic (HEAT) +SF3B1 ENST00000335508.11 frameshift_variant likely benign +SF3B1 ENST00000335508.11 stop_gained likely benign +SF3B1 ENST00000335508.11 stop_lost likely benign +SF3B1 ENST00000335508.11 likely benign +SRSF2 ENST00000359995.10 missense_variant 283 288 pathogenic +SRSF2 ENST00000359995.10 inframe_insertion 283 288 pathogenic +SRSF2 ENST00000359995.10 inframe_deletion 283 288 pathogenic +SRSF2 ENST00000359995.10 protein_altering_variant 283 288 pathogenic +SRSF2 ENST00000359995.10 likely benign STAG2 ENST00000371145.8 frameshift_variant pathogenic STAG2 ENST00000371145.8 start_lost pathogenic STAG2 ENST00000371145.8 stop_gained pathogenic STAG2 ENST00000371145.8 stop_lost pathogenic -STAG2 ENST00000371145.8 splice_acceptor_variant pathogenic -STAG2 ENST00000371145.8 splice_donor_variant pathogenic +STAG2 ENST00000371145.8 possible pathogenic U2AF1 ENST00000291552.9 missense_variant 100 105 possible pathogenic U2AF1 ENST00000291552.9 inframe_insertion 100 105 possible pathogenic U2AF1 ENST00000291552.9 inframe_deletion 100 105 possible pathogenic +U2AF1 ENST00000291552.9 protein_altering_variant 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 +U2AF1 ENST00000291552.9 protein_altering_variant 466 477 possible pathogenic +U2AF1 ENST00000291552.9 likely benign ZRSR2 ENST00000307771.8 frameshift_variant pathogenic ZRSR2 ENST00000307771.8 start_lost pathogenic ZRSR2 ENST00000307771.8 stop_gained pathogenic ZRSR2 ENST00000307771.8 stop_lost pathogenic -ZRSR2 ENST00000307771.8 splice_acceptor_variant pathogenic -ZRSR2 ENST00000307771.8 splice_donor_variant pathogenic +ZRSR2 ENST00000307771.8 possible pathogenic TP53 ENST00000269305.9 frameshift_variant pathogenic TP53 ENST00000269305.9 start_lost pathogenic TP53 ENST00000269305.9 stop_gained pathogenic @@ -76,117 +94,148 @@ TP53 ENST00000269305.9 missense_variant 742 744 pathogenic TP53 ENST00000269305.9 missense_variant possible pathogenic TP53 ENST00000269305.9 inframe_insertion possible pathogenic TP53 ENST00000269305.9 inframe_deletion possible pathogenic +TP53 ENST00000269305.9 protein_altering_variant possible pathogenic TP53g ENST00000455263.6 994-2 *2 possible pathogenic (alt exon 10 gamma) TP53b ENST00000420246.6 994-2 *2 possible pathogenic (alt exon 10 beta) NRAS ENST00000369535.5 missense_variant 34 39 pathogenic -NRAS ENST00000369535.5 inframe_insertion 34 39 possible pathogenic -NRAS ENST00000369535.5 inframe_deletion 34 39 possible pathogenic NRAS ENST00000369535.5 missense_variant 181 183 pathogenic -NRAS ENST00000369535.5 inframe_insertion 181 183 possible pathogenic -NRAS ENST00000369535.5 inframe_deletion 181 183 possible pathogenic -NRAS ENST00000369535.5 frameshift_variant discard -NRAS ENST00000369535.5 stop_gained discard -NRAS ENST00000369535.5 stop_lost discard -KRAS ENST00000256078.10 missense_variant 1 290 possible pathogenic -KRAS ENST00000256078.10 inframe_insertion 1 290 possible pathogenic -KRAS ENST00000256078.10 inframe_deletion 1 290 possible pathogenic -KRAS ENST00000256078.10 frameshift_variant discard -KRAS ENST00000256078.10 stop_gained discard -KRAS ENST00000256078.10 stop_lost discard +NRAS ENST00000369535.5 missense_variant possible pathogenic +NRAS ENST00000369535.5 inframe_insertion possible pathogenic +NRAS ENST00000369535.5 inframe_deletion possible pathogenic +NRAS ENST00000369535.5 protein_altering_variant possible pathogenic +NRAS ENST00000369535.5 frameshift_variant likely benign +NRAS ENST00000369535.5 stop_gained likely benign +NRAS ENST00000369535.5 stop_lost likely benign +KRAS ENST00000256078.10 missense_variant 34 39 pathogenic +KRAS ENST00000256078.10 missense_variant 181 183 pathogenic +KRAS ENST00000256078.10 missense_variant possible pathogenic +KRAS ENST00000256078.10 inframe_insertion possible pathogenic +KRAS ENST00000256078.10 inframe_deletion possible pathogenic +KRAS ENST00000256078.10 protein_altering_variant possible pathogenic +KRAS ENST00000256078.10 frameshift_variant likely benign +KRAS ENST00000256078.10 stop_gained likely benign +KRAS ENST00000256078.10 stop_lost likely benign DDX41 ENST00000330503.12 missense_variant 1291 1701 likely pathogenic +DDX41 ENST00000330503.12 possible pathogenic KIT ENST00000288135.6 inframe_deletion 1246 1257 pathogenic KIT ENST00000288135.6 inframe_insertion 1246 1257 pathogenic KIT ENST00000288135.6 missense_variant 2447 2449 pathogenic KIT ENST00000288135.6 missense_variant 2465 2467 pathogenic -KIT ENST00000288135.6 frameshift_variant discard -KIT ENST00000288135.6 stop_gained discard -KIT ENST00000288135.6 stop_lost discard +KIT ENST00000288135.6 inframe_deletion possible pathogenic +KIT ENST00000288135.6 inframe_insertion possible pathogenic +KIT ENST00000288135.6 missense_variant possible pathogenic +KIT ENST00000288135.6 protein_altering_variant possible pathogenic +KIT ENST00000288135.6 frameshift_variant likely benign +KIT ENST00000288135.6 stop_gained likely benign +KIT ENST00000288135.6 stop_lost likely benign 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 +BRAF ENST00000646891.2 protein_altering_variant 1768 1845 possible pathogenic +BRAF ENST00000646891.2 likely benign 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 +CALR ENST00000316448.10 likely benign +CBL ENST00000264033.6 missense_variant 1099 1101 likely pathogenic +CBL ENST00000264033.6 missense_variant 1111 1113 likely pathogenic +CBL ENST00000264033.6 missense_variant 1141 1152 likely pathogenic +CBL ENST00000264033.6 missense_variant 1186 1188 likely pathogenic +CBL ENST00000264033.6 missense_variant 1192 1194 likely pathogenic +CBL ENST00000264033.6 missense_variant 1210 1212 likely pathogenic +CBL ENST00000264033.6 missense_variant 1222 1224 likely pathogenic +CBL ENST00000264033.6 missense_variant 1246 1254 likely pathogenic +CBL ENST00000264033.6 missense_variant 1258 1260 likely pathogenic CBL ENST00000264033.6 1096-2 1431+2 possible pathogenic (RING fingers) +CBL ENST00000264033.6 likely benign 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 +CSF3R ENST00000373103.5 missense_variant 1724 1864 possible pathogenic (exon 14 activating) +CSF3R ENST00000373103.5 likely benign DNMT3A ENST00000321117.10 missense_variant 2644 2645 pathogenic +DNMT3A ENST00000321117.10 frameshift_variant likely pathogenic +DNMT3A ENST00000321117.10 stop_gained likely pathogenic +DNMT3A ENST00000321117.10 stop_lost likely 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_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) +DNMT3A ENST00000321117.10 protein_altering_variant possible pathogenic +ETNK1 ENST00000671733.1 likely benign (not known pathogenic) +ETV6 ENST00000396373.9 frameshift_variant likely pathogenic +ETV6 ENST00000396373.9 stop_gained likely pathogenic +ETV6 ENST00000396373.9 stop_glost likely pathogenic ETV6 ENST00000396373.9 missense_variant possible pathogenic ETV6 ENST00000396373.9 inframe_insertion possible pathogenic ETV6 ENST00000396373.9 inframe_deletion possible pathogenic -ETV6 ENST00000396373.9 likely pathogenic +ETV6 ENST00000396373.9 protein_altering_variant possible pathogenic GATA2 ENST00000341105.7 frameshift_variant -2 871+2 pathogenic GATA2 ENST00000341105.7 stop_gained -2 871+2 pathogenic GATA2 ENST00000341105.7 stop_lost -2 871+2 pathogenic -GATA2 ENST00000341105.7 splice_donor_variant -2 871+2 pathogenic -GATA2 ENST00000341105.7 splice_acceptor_variant -2 871+2 pathogenic GATA2 ENST00000341105.7 likely pathogenic IDH1 ENST00000345146.7 missense_variant 394 395 pathogenic +IDH1 ENST00000345146.7 likely benign IDH2 ENST00000330062.8 missense_variant 418 420 pathogenic IDH2 ENST00000330062.8 missense_variant 514 516 pathogenic +IDH2 ENST00000330062.8 likely benign JAK2 ENST00000381652.4 missense_variant 1514 1641 likely pathogenic JAK2 ENST00000381652.4 inframe_insertion 1514 1641 likely pathogenic JAK2 ENST00000381652.4 inframe_deletion 1514 1641 likely pathogenic -JAK2 ENST00000381652.4 frameshift_variant discard -JAK2 ENST00000381652.4 stop_gained discard -JAK2 ENST00000381652.4 stop_lost discard +JAK2 ENST00000381652.4 protein_altering_variant 1514 1641 likely pathogenic +JAK2 ENST00000381652.4 frameshift_variant likely benign +JAK2 ENST00000381652.4 stop_gained likely benign +JAK2 ENST00000381652.4 stop_lost likely benign +JAK2 ENST00000381652.4 likely benign NFE2 ENST00000435572.7 frameshift_variant likely pathogenic NFE2 ENST00000435572.7 start_lost likely pathogenic NFE2 ENST00000435572.7 stop_gained likely pathogenic NFE2 ENST00000435572.7 stop_lost likely pathogenic NFE2 ENST00000435572.7 possible pathogenic -PHF6 ENST00000332070.7 start_lost likely pathogenic +PHF6 ENST00000332070.7 frameshift_variant likely pathogenic PHF6 ENST00000332070.7 stop_gained likely pathogenic PHF6 ENST00000332070.7 stop_lost likely pathogenic -PHF6 ENST00000332070.7 splice_acceptor_variant likely pathogenic -PHF6 ENST00000332070.7 splice_donor_variant likely pathogenic PHF6 ENST00000332070.7 possible pathogenic PPM1D ENST00000305921.8 frameshift_variant 1261-2 *2 pathogenic PPM1D ENST00000305921.8 stop_gained 1261-2 *2 pathogenic PPM1D ENST00000305921.8 stop_lost 1261-2 *2 pathogenic PPM1D ENST00000305921.8 start_lost 1261-2 *2 pathogenic -PPM1D ENST00000305921.8 splice_acceptor_variant 1261-2 *2 pathogenic -PPM1D ENST00000305921.8 splice_donor_variant 1261-2 *2 pathogenic +PPM1D ENST00000305921.8 likely benign PTPN11 ENST00000351677.7 missense_variant 138 332 likely pathogenic -PTPN11 ENST00000351677.7 inframe_deletion 138 332 likely pathogenic -PTPN11 ENST00000351677.7 inframe_insertion 138 332 likely pathogenic +PTPN11 ENST00000351677.7 inframe_deletion 138 332 possible pathogenic +PTPN11 ENST00000351677.7 inframe_insertion 138 332 possible pathogenic +PTPN11 ENST00000351677.7 protein_altering_variant 138 332 possible pathogenic PTPN11 ENST00000351677.7 missense_variant 1448 1599 likely pathogenic -PTPN11 ENST00000351677.7 inframe_insertion 1448 1599 likely pathogenic -PTPN11 ENST00000351677.7 inframe_deletion 1448 1599 likely pathogenic -PTPN11 ENST00000351677.7 frameshift_variant discard -PTPN11 ENST00000351677.7 stop_gained discard -PTPN11 ENST00000351677.7 stop_lost discard +PTPN11 ENST00000351677.7 inframe_insertion 1448 1599 possible pathogenic +PTPN11 ENST00000351677.7 inframe_deletion 1448 1599 possible pathogenic +PTPN11 ENST00000351677.7 protein_altering_variant 1448 1599 possible pathogenic +PTPN11 ENST00000351677.7 frameshift_variant likely benign +PTPN11 ENST00000351677.7 stop_gained likely benign +PTPN11 ENST00000351677.7 stop_lost likely benign +PTPN11 ENST00000351677.7 likely benign SETBP1 ENST00000649279.2 missense_variant 2548 2730 possible pathogenic -SETBP1 ENST00000649279.2 discard +SETBP1 ENST00000649279.2 likely benign 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) -UBA1 ENST00000335972.11 discard (only known pathogenic) +TET2 ENST00000380013.9 possible pathogenic +UBA1 ENST00000335972.11 missense_variant 118 176 possible pathogenic (if VEXAS) +UBA1 ENST00000335972.11 likely benign WT1 ENST00000452863.10 frameshift_variant 1114 1264 pathogenic WT1 ENST00000452863.10 start_lost 1114 1264 pathogenic WT1 ENST00000452863.10 stop_gained 1114 1264 pathogenic -WT1 ENST00000452863.10 stop_lost 1114-2 1264+2 pathogenic +WT1 ENST00000452863.10 stop_lost 1114 1264 pathogenic +WT1 ENST00000452863.10 1114 1264 possible pathogenic WT1 ENST00000452863.10 missense_variant 1357 1446 possible pathogenic +WT1 ENST00000452863.10 1357 1446 possible pathogenic +WT1 ENST00000452863.10 likely benign +MPL ENST00000372470.9 likely benign (not known pathogenic) BCORL1 ENST00000540052.6 possible pathogenic CUX1 ENST00000292535.12 possible pathogenic 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 \ No newline at end of file +RAD21 ENST00000297338.7 possible pathogenic diff --git a/utilities/deps/small-files/inclusion_criteria.tsv b/utilities/deps/small-files/inclusion_criteria.tsv index 6962f353..6737ba3e 100644 --- a/utilities/deps/small-files/inclusion_criteria.tsv +++ b/utilities/deps/small-files/inclusion_criteria.tsv @@ -167,7 +167,6 @@ BCORL1 ENST00000540052.6 inframe_insertion BCORL1 ENST00000540052.6 inframe_deletion BCORL1 ENST00000540052.6 protein_altering_variant BCORL1 ENST00000540052.6 missense_variant -BCORL1 ENST00000540052.6 stop_gained BRAF ENST00000646891.2 stop_gained BRAF ENST00000646891.2 frameshift_variant BRAF ENST00000646891.2 stop_lost @@ -176,7 +175,6 @@ BRAF ENST00000646891.2 inframe_insertion BRAF ENST00000646891.2 inframe_deletion BRAF ENST00000646891.2 protein_altering_variant BRAF ENST00000646891.2 missense_variant -BRAF ENST00000646891.2 stop_gained CALR ENST00000316448.10 stop_gained CALR ENST00000316448.10 frameshift_variant CALR ENST00000316448.10 stop_lost @@ -185,7 +183,6 @@ CALR ENST00000316448.10 inframe_insertion CALR ENST00000316448.10 inframe_deletion CALR ENST00000316448.10 protein_altering_variant CALR ENST00000316448.10 missense_variant -CALR ENST00000316448.10 stop_gained CBL ENST00000264033.6 stop_gained CBL ENST00000264033.6 frameshift_variant CBL ENST00000264033.6 stop_lost @@ -194,7 +191,6 @@ CBL ENST00000264033.6 inframe_insertion CBL ENST00000264033.6 inframe_deletion CBL ENST00000264033.6 protein_altering_variant CBL ENST00000264033.6 missense_variant -CBL ENST00000264033.6 stop_gained CSF3R ENST00000373103.5 stop_gained CSF3R ENST00000373103.5 frameshift_variant CSF3R ENST00000373103.5 stop_lost @@ -203,7 +199,6 @@ CSF3R ENST00000373103.5 inframe_insertion CSF3R ENST00000373103.5 inframe_deletion CSF3R ENST00000373103.5 protein_altering_variant CSF3R ENST00000373103.5 missense_variant -CSF3R ENST00000373103.5 stop_gained CUX1 ENST00000292535.12 stop_gained CUX1 ENST00000292535.12 frameshift_variant CUX1 ENST00000292535.12 stop_lost @@ -212,7 +207,6 @@ CUX1 ENST00000292535.12 inframe_insertion CUX1 ENST00000292535.12 inframe_deletion CUX1 ENST00000292535.12 protein_altering_variant CUX1 ENST00000292535.12 missense_variant -CUX1 ENST00000292535.12 stop_gained DDX41 ENST00000330503.12 stop_gained DDX41 ENST00000330503.12 frameshift_variant DDX41 ENST00000330503.12 stop_lost @@ -221,7 +215,6 @@ DDX41 ENST00000330503.12 inframe_insertion DDX41 ENST00000330503.12 inframe_deletion DDX41 ENST00000330503.12 protein_altering_variant DDX41 ENST00000330503.12 missense_variant -DDX41 ENST00000330503.12 stop_gained ETNK1 ENST00000671733.1 stop_gained ETNK1 ENST00000671733.1 frameshift_variant ETNK1 ENST00000671733.1 stop_lost @@ -230,7 +223,6 @@ ETNK1 ENST00000671733.1 inframe_insertion ETNK1 ENST00000671733.1 inframe_deletion ETNK1 ENST00000671733.1 protein_altering_variant ETNK1 ENST00000671733.1 missense_variant -ETNK1 ENST00000671733.1 stop_gained ETV6 ENST00000396373.9 stop_gained ETV6 ENST00000396373.9 frameshift_variant ETV6 ENST00000396373.9 stop_lost @@ -239,7 +231,6 @@ ETV6 ENST00000396373.9 inframe_insertion ETV6 ENST00000396373.9 inframe_deletion ETV6 ENST00000396373.9 protein_altering_variant ETV6 ENST00000396373.9 missense_variant -ETV6 ENST00000396373.9 stop_gained GATA2 ENST00000341105.7 stop_gained GATA2 ENST00000341105.7 frameshift_variant GATA2 ENST00000341105.7 stop_lost @@ -248,7 +239,6 @@ GATA2 ENST00000341105.7 inframe_insertion GATA2 ENST00000341105.7 inframe_deletion GATA2 ENST00000341105.7 protein_altering_variant GATA2 ENST00000341105.7 missense_variant -GATA2 ENST00000341105.7 stop_gained GNB1 ENST00000378609.9 stop_gained GNB1 ENST00000378609.9 frameshift_variant GNB1 ENST00000378609.9 stop_lost @@ -257,7 +247,6 @@ GNB1 ENST00000378609.9 inframe_insertion GNB1 ENST00000378609.9 inframe_deletion GNB1 ENST00000378609.9 protein_altering_variant GNB1 ENST00000378609.9 missense_variant -GNB1 ENST00000378609.9 stop_gained JAK2 ENST00000381652.4 stop_gained JAK2 ENST00000381652.4 frameshift_variant JAK2 ENST00000381652.4 stop_lost @@ -266,7 +255,6 @@ JAK2 ENST00000381652.4 inframe_insertion JAK2 ENST00000381652.4 inframe_deletion JAK2 ENST00000381652.4 protein_altering_variant JAK2 ENST00000381652.4 missense_variant -JAK2 ENST00000381652.4 stop_gained KRAS ENST00000256078.10 stop_gained KRAS ENST00000256078.10 frameshift_variant KRAS ENST00000256078.10 stop_lost @@ -275,7 +263,6 @@ KRAS ENST00000256078.10 inframe_insertion KRAS ENST00000256078.10 inframe_deletion KRAS ENST00000256078.10 protein_altering_variant KRAS ENST00000256078.10 missense_variant -KRAS ENST00000256078.10 stop_gained MYC ENST00000621592.8 stop_gained MYC ENST00000621592.8 frameshift_variant MYC ENST00000621592.8 stop_lost @@ -284,7 +271,6 @@ MYC ENST00000621592.8 inframe_insertion MYC ENST00000621592.8 inframe_deletion MYC ENST00000621592.8 protein_altering_variant MYC ENST00000621592.8 missense_variant -MYC ENST00000621592.8 stop_gained NF1 ENST00000358273.9 stop_gained NF1 ENST00000358273.9 frameshift_variant NF1 ENST00000358273.9 stop_lost @@ -293,7 +279,6 @@ NF1 ENST00000358273.9 inframe_insertion NF1 ENST00000358273.9 inframe_deletion NF1 ENST00000358273.9 protein_altering_variant NF1 ENST00000358273.9 missense_variant -NF1 ENST00000358273.9 stop_gained NFE2 ENST00000435572.7 stop_gained NFE2 ENST00000435572.7 frameshift_variant NFE2 ENST00000435572.7 stop_lost @@ -302,7 +287,6 @@ NFE2 ENST00000435572.7 inframe_insertion NFE2 ENST00000435572.7 inframe_deletion NFE2 ENST00000435572.7 protein_altering_variant NFE2 ENST00000435572.7 missense_variant -NFE2 ENST00000435572.7 stop_gained PHF6 ENST00000332070.7 stop_gained PHF6 ENST00000332070.7 frameshift_variant PHF6 ENST00000332070.7 stop_lost @@ -311,7 +295,6 @@ PHF6 ENST00000332070.7 inframe_insertion PHF6 ENST00000332070.7 inframe_deletion PHF6 ENST00000332070.7 protein_altering_variant PHF6 ENST00000332070.7 missense_variant -PHF6 ENST00000332070.7 stop_gained PPM1D ENST00000305921.8 stop_gained PPM1D ENST00000305921.8 frameshift_variant PPM1D ENST00000305921.8 stop_lost @@ -320,7 +303,6 @@ PPM1D ENST00000305921.8 inframe_insertion PPM1D ENST00000305921.8 inframe_deletion PPM1D ENST00000305921.8 protein_altering_variant PPM1D ENST00000305921.8 missense_variant -PPM1D ENST00000305921.8 stop_gained PRPF8 ENST00000304992.11 stop_gained PRPF8 ENST00000304992.11 frameshift_variant PRPF8 ENST00000304992.11 stop_lost @@ -329,7 +311,6 @@ PRPF8 ENST00000304992.11 inframe_insertion PRPF8 ENST00000304992.11 inframe_deletion PRPF8 ENST00000304992.11 protein_altering_variant PRPF8 ENST00000304992.11 missense_variant -PRPF8 ENST00000304992.11 stop_gained PTPN11 ENST00000351677.7 stop_gained PTPN11 ENST00000351677.7 frameshift_variant PTPN11 ENST00000351677.7 stop_lost @@ -338,7 +319,6 @@ PTPN11 ENST00000351677.7 inframe_insertion PTPN11 ENST00000351677.7 inframe_deletion PTPN11 ENST00000351677.7 protein_altering_variant PTPN11 ENST00000351677.7 missense_variant -PTPN11 ENST00000351677.7 stop_gained RAD21 ENST00000297338.7 stop_gained RAD21 ENST00000297338.7 frameshift_variant RAD21 ENST00000297338.7 stop_lost @@ -347,16 +327,14 @@ RAD21 ENST00000297338.7 inframe_insertion RAD21 ENST00000297338.7 inframe_deletion RAD21 ENST00000297338.7 protein_altering_variant RAD21 ENST00000297338.7 missense_variant -RAD21 ENST00000297338.7 stop_gained -RUNX1b ENST00000344691.8 stop_gained -RUNX1b ENST00000344691.8 frameshift_variant -RUNX1b ENST00000344691.8 stop_lost -RUNX1b ENST00000344691.8 start_lost -RUNX1b ENST00000344691.8 inframe_insertion -RUNX1b ENST00000344691.8 inframe_deletion -RUNX1b ENST00000344691.8 protein_altering_variant -RUNX1b ENST00000344691.8 missense_variant -RUNX1b ENST00000344691.8 stop_gained +RUNX1b ENST00000344691.8 stop_gained -2 270+2 +RUNX1b ENST00000344691.8 frameshift_variant -2 270+2 +RUNX1b ENST00000344691.8 stop_lost -2 270+2 +RUNX1b ENST00000344691.8 start_lost -2 270+2 +RUNX1b ENST00000344691.8 inframe_insertion -2 270+2 +RUNX1b ENST00000344691.8 inframe_deletion -2 270+2 +RUNX1b ENST00000344691.8 protein_altering_variant -2 270+2 +RUNX1b ENST00000344691.8 missense_variant -2 270+2 SETBP1 ENST00000649279.2 stop_gained SETBP1 ENST00000649279.2 frameshift_variant SETBP1 ENST00000649279.2 stop_lost @@ -365,25 +343,22 @@ SETBP1 ENST00000649279.2 inframe_insertion SETBP1 ENST00000649279.2 inframe_deletion SETBP1 ENST00000649279.2 protein_altering_variant SETBP1 ENST00000649279.2 missense_variant -SETBP1 ENST00000649279.2 stop_gained -TP53b ENST00000420246.6 stop_gained -TP53b ENST00000420246.6 frameshift_variant -TP53b ENST00000420246.6 stop_lost -TP53b ENST00000420246.6 start_lost -TP53b ENST00000420246.6 inframe_insertion -TP53b ENST00000420246.6 inframe_deletion -TP53b ENST00000420246.6 protein_altering_variant -TP53b ENST00000420246.6 missense_variant -TP53b ENST00000420246.6 stop_gained -TP53g ENST00000455263.6 stop_gained -TP53g ENST00000455263.6 frameshift_variant -TP53g ENST00000455263.6 stop_lost -TP53g ENST00000455263.6 start_lost -TP53g ENST00000455263.6 inframe_insertion -TP53g ENST00000455263.6 inframe_deletion -TP53g ENST00000455263.6 protein_altering_variant -TP53g ENST00000455263.6 missense_variant -TP53g ENST00000455263.6 stop_gained +TP53b ENST00000420246.6 stop_gained 994-2 *2 +TP53b ENST00000420246.6 frameshift_variant 994-2 *2 +TP53b ENST00000420246.6 stop_lost 994-2 *2 +TP53b ENST00000420246.6 start_lost 994-2 *2 +TP53b ENST00000420246.6 inframe_insertion 994-2 *2 +TP53b ENST00000420246.6 inframe_deletion 994-2 *2 +TP53b ENST00000420246.6 protein_altering_variant 994-2 *2 +TP53b ENST00000420246.6 missense_variant 994-2 *2 +TP53g ENST00000455263.6 stop_gained 994-2 *2 +TP53g ENST00000455263.6 frameshift_variant 994-2 *2 +TP53g ENST00000455263.6 stop_lost 994-2 *2 +TP53g ENST00000455263.6 start_lost 994-2 *2 +TP53g ENST00000455263.6 inframe_insertion 994-2 *2 +TP53g ENST00000455263.6 inframe_deletion 994-2 *2 +TP53g ENST00000455263.6 protein_altering_variant 994-2 *2 +TP53g ENST00000455263.6 missense_variant 994-2 *2 UBA1 ENST00000335972.11 frameshift_variant UBA1 ENST00000335972.11 stop_lost UBA1 ENST00000335972.11 start_lost @@ -392,3 +367,11 @@ UBA1 ENST00000335972.11 inframe_deletion UBA1 ENST00000335972.11 protein_altering_variant UBA1 ENST00000335972.11 missense_variant UBA1 ENST00000335972.11 stop_gained +MPL ENST00000372470.9 frameshift_variant +MPL ENST00000372470.9 inframe_deletion +MPL ENST00000372470.9 inframe_insertion +MPL ENST00000372470.9 missense_variant +MPL ENST00000372470.9 protein_altering_variant +MPL ENST00000372470.9 start_lost +MPL ENST00000372470.9 stop_gained +MPL ENST00000372470.9 stop_lost diff --git a/utilities/deps/small-files/known_variants.tsv b/utilities/deps/small-files/known_variants.tsv index 659ef147..38779bae 100644 --- a/utilities/deps/small-files/known_variants.tsv +++ b/utilities/deps/small-files/known_variants.tsv @@ -1,4 +1,11 @@ gene_name variant annotation +ASXL1 ENST00000375687.10:c.1772dup known pathogenic +ASXL1 ENST00000375687.10:c.1773C>A known pathogenic +ASXL1 ENST00000375687.10:c.1773C>G known pathogenic +ASXL1 ENST00000375687.10:c.1900_1922del known pathogenic +ASXL1 ENST00000375687.10:c.1934dup known pathogenic (check artifact!) +ASXL1 ENST00000375687.10:c.2077C>T known pathogenic +ASXL1 ENST00000375687.10:c.3202C>T known pathogenic BRAF ENST00000646891.2:c.1781A>G known pathogenic BRAF ENST00000646891.2:c.1799T>A known pathogenic BRAF ENST00000646891.2:c.1799T>G known pathogenic @@ -18,11 +25,22 @@ CBL ENST00000264033.6:c.1186T>C known pathogenic CBL ENST00000264033.6:c.1211G>A known pathogenic CBL ENST00000264033.6:c.1258C>T known pathogenic CBL ENST00000264033.6:c.1259G>A known pathogenic +CEBPA ENST00000498907.3:c.247del known pathogenic +CEBPA ENST00000498907.3:c.912_913insTTG known pathogenic +CEBPA ENST00000498907.3:c.934_936dup known pathogenic +CEBPA ENST00000498907.3:c.937_939dup known pathogenic +CEBPA ENST00000498907.3:c.940_941insAAG known pathogenic CSF3R ENST00000373103.5:c.1843A>G known pathogenic (exon 14 activating) CSF3R ENST00000373103.5:c.1853C>T known pathogenic (exon 14 activating) DDX41 ENST00000330503.12:c.3G>A known pathogenic (germline) DDX41 ENST00000330503.12:c.415_418dup known pathogenic (germline) DDX41 ENST00000330503.12:c.1574G>A known pathogenic +DNMT3A ENST00000321117.10:c.2644C>A known pathogenic +DNMT3A ENST00000321117.10:c.2644C>G known pathogenic +DNMT3A ENST00000321117.10:c.2644C>T known pathogenic +DNMT3A ENST00000321117.10:c.2645G>A known pathogenic +DNMT3A ENST00000321117.10:c.2645G>C known pathogenic +DNMT3A ENST00000321117.10:c.2645G>T known pathogenic ETNK1 ENST00000671733.1:c.727C>T known pathogenic ETNK1 ENST00000671733.1:c.730A>C known pathogenic ETNK1 ENST00000671733.1:c.731A>G known pathogenic @@ -66,6 +84,12 @@ FLT3 ENST00000241453.12:c.2521A>C known pathogenic (TKD) FLT3 ENST00000241453.12:c.2523C>A known pathogenic (TKD) FLT3 ENST00000241453.12:c.2524T>C known pathogenic (TKD) FLT3 ENST00000241453.12:c.2525A>G known pathogenic (TKD) +IDH1 ENST00000345146.7:c.394C>A known pathogenic +IDH1 ENST00000345146.7:c.394C>G known pathogenic +IDH1 ENST00000345146.7:c.394C>T known pathogenic +IDH1 ENST00000345146.7:c.395G>A known pathogenic +IDH1 ENST00000345146.7:c.395G>C known pathogenic +IDH1 ENST00000345146.7:c.395G>T known pathogenic IDH2 ENST00000330062.8:c.418C>G known pathogenic IDH2 ENST00000330062.8:c.418C>T known pathogenic IDH2 ENST00000330062.8:c.419G>A known pathogenic @@ -117,6 +141,7 @@ MPL ENST00000372470.9:c.1543_1544delinsAA known pathogenic MPL ENST00000372470.9:c.1543_1544delinsGC known pathogenic MPL ENST00000372470.9:c.1543_1545delinsAAA known pathogenic MPL ENST00000372470.9:c.1544G>T known pathogenic +MPL ENST00000372470.9:c.1502T>C known pathogenic (if also Trp515) MPL ENST00000372470.9:c.1514G>A known pathogenic NFE2 ENST00000435572.7:c.782_785del known pathogenic NPM1 ENST00000296930.10:c.860_863dup known pathogenic (type A) @@ -125,6 +150,24 @@ NPM1 ENST00000296930.10:c.863_864insCCAG known pathogenic (type N) NPM1 ENST00000296930.10:c.863_864insCCTG known pathogenic (type D) NPM1 ENST00000296930.10:c.863_864insCTTG known pathogenic (type P) NPM1 ENST00000296930.10:c.863_864insTATG known pathogenic (type J) +NPM1 ENST00000296930.10:c.861_862delinsTTGTCA known pathogenic +NPM1 ENST00000296930.10:c.862delinsATTCG known pathogenic +NPM1 ENST00000296930.10:c.863_864insCAGG known pathogenic +NPM1 ENST00000296930.10:c.863_864insCCGG known pathogenic +NPM1 ENST00000296930.10:c.863_864insCGTG known pathogenic +NPM1 ENST00000296930.10:c.863_864insTCGG known pathogenic +NPM1 ENST00000296930.10:c.863_864insTTCG known pathogenic +NPM1 ENST00000296930.10:c.863_864insTTTG known pathogenic +NPM1 ENST00000296930.10:c.864_865delinsCCGCGG known pathogenic +NPM1 ENST00000296930.10:c.867_868insAGGA known pathogenic +NPM1 ENST00000296930.10:c.867_871delinsAAGGTTAGC known pathogenic +NPM1 ENST00000296930.10:c.868_869delinsCGATTT known pathogenic +NPM1 ENST00000296930.10:c.868_870delinsCGATTCC known pathogenic +NPM1 ENST00000296930.10:c.869_873delinsCCCTGGAGA known pathogenic +NPM1 ENST00000296930.10:c.869_873delinsCCCTGTCGA known pathogenic +NPM1 ENST00000296930.10:c.869_873delinsCCCTTTCCC known pathogenic +NPM1 ENST00000296930.10:c.869_873delinsCTCTTGCCC known pathogenic +NPM1 ENST00000296930.10:c.869_873delinsCTTTCTCCC known pathogenic NRAS ENST00000369535.5:c.34G>A known pathogenic NRAS ENST00000369535.5:c.34G>C known pathogenic NRAS ENST00000369535.5:c.34G>T known pathogenic @@ -143,7 +186,10 @@ NRAS ENST00000369535.5:c.183A>C known pathogenic NRAS ENST00000369535.5:c.183A>T known pathogenic NRAS ENST00000369535.5:c.175G>A known pathogenic NRAS ENST00000369535.5:c.176C>A known pathogenic +RUNX1 ENST00000675419.1:c.496C>T known pathogenic +RUNX1 ENST00000675419.1:c.601C>T known pathogenic RUNX1 ENST00000675419.1:c.602G>A known pathogenic +RUNX1 ENST00000675419.1:c.610C>T known pathogenic RUNX1 ENST00000675419.1:c.611G>A known pathogenic RUNX1 ENST00000675419.1:c.319C>A known pathogenic RUNX1 ENST00000675419.1:c.319C>T known pathogenic @@ -157,9 +203,12 @@ RUNX1 ENST00000675419.1:c.592G>A known pathogenic RUNX1 ENST00000675419.1:c.593A>G known pathogenic RUNX1 ENST00000675419.1:c.593A>T known pathogenic RUNX1 ENST00000675419.1:c.601C>G known pathogenic +RUNX1 ENST00000675419.1:c.609dup known pathogenic RUNX1 ENST00000675419.1:c.611G>T known pathogenic +RUNX1 ENST00000675419.1:c.618_621dup known pathogenic RUNX1 ENST00000675419.1:c.619C>T known pathogenic RUNX1 ENST00000675419.1:c.620G>A known pathogenic +RUNX1 ENST00000675419.1:c.958C>T known pathogenic SETBP1 ENST00000649279.2:c.2602G>A known pathogenic SETBP1 ENST00000649279.2:c.2603A>C known pathogenic SETBP1 ENST00000649279.2:c.2608G>A known pathogenic @@ -188,10 +237,22 @@ SF3B1 ENST00000335508.11:c.2098A>G known pathogenic SF3B1 ENST00000335508.11:c.2225G>A known pathogenic SF3B1 ENST00000335508.11:c.2342A>G known pathogenic SRSF2 ENST00000359995.10:c.281_283dup known pathogenic +SRSF2 ENST00000359995.10:c.283C>A known pathogenic +SRSF2 ENST00000359995.10:c.283C>G known pathogenic +SRSF2 ENST00000359995.10:c.283_291del known pathogenic +SRSF2 ENST00000359995.10:c.284C>A known pathogenic +SRSF2 ENST00000359995.10:c.284C>G known pathogenic +SRSF2 ENST00000359995.10:c.284C>T known pathogenic +SRSF2 ENST00000359995.10:c.284_298del known pathogenic +SRSF2 ENST00000359995.10:c.284_304del known pathogenic +SRSF2 ENST00000359995.10:c.284_307del known pathogenic SRSF2 ENST00000359995.10:c.287C>T known pathogenic +TET2 ENST00000380013.9:c.3646C>T known pathogenic TET2 ENST00000380013.9:c.3782G>A known pathogenic TET2 ENST00000380013.9:c.3812G>C known pathogenic TET2 ENST00000380013.9:c.4075C>T known pathogenic +TET2 ENST00000380013.9:c.4393C>T known pathogenic +TET2 ENST00000380013.9:c.4546C>T known pathogenic TET2 ENST00000380013.9:c.5618T>C known pathogenic TP53 ENST00000269305.9:c.524G>A known pathogenic TP53 ENST00000269305.9:c.536A>G known pathogenic @@ -202,6 +263,7 @@ TP53 ENST00000269305.9:c.742C>T known pathogenic TP53 ENST00000269305.9:c.743G>A known pathogenic TP53 ENST00000269305.9:c.814G>A known pathogenic TP53 ENST00000269305.9:c.818G>A known pathogenic +TP53 ENST00000269305.9:c.916C>T known pathogenic TP53 ENST00000269305.9:c.488A>G known pathogenic TP53 ENST00000269305.9:c.559+1G>A known pathogenic TP53 ENST00000269305.9:c.658T>C known pathogenic @@ -218,9 +280,12 @@ UBA1 ENST00000335972.11:c.121A>G known pathogenic (VEXAS) UBA1 ENST00000335972.11:c.122T>C known pathogenic (VEXAS) UBA1 ENST00000335972.11:c.118-1G>C known pathogenic (VEXAS) UBA1 ENST00000335972.11:c.167C>T known pathogenic (VEXAS) +WT1 ENST00000452863.10:c.1387C>T known pathogenic WT1 ENST00000452863.10:c.1399C>T known pathogenic WT1 ENST00000452863.10:c.1400G>C known pathogenic +WT1 ENST00000452863.10:c.1125dup known pathogenic WT1 ENST00000452863.10:c.1153C>G known pathogenic +WT1 ENST00000452863.10:c.1157C>A known pathogenic FLT3 ENST00000241453.12:c.2127dup artifact FLT3 ENST00000241453.12:c.2317dup artifact FLT3 ENST00000241453.12:c.52dup artifact