From c545f4c9dbda9b1a4f63a36079e2c1d1ea53d6c9 Mon Sep 17 00:00:00 2001 From: acvandergrinten Date: Tue, 7 Oct 2025 09:28:09 +0200 Subject: [PATCH 1/5] update AML variant annotation criteria --- .../deps/small-files/annotation_criteria.tsv | 220 +++++++++++++++--- 1 file changed, 192 insertions(+), 28 deletions(-) diff --git a/utilities/deps/small-files/annotation_criteria.tsv b/utilities/deps/small-files/annotation_criteria.tsv index b7793859..ea4d700f 100644 --- a/utilities/deps/small-files/annotation_criteria.tsv +++ b/utilities/deps/small-files/annotation_criteria.tsv @@ -1,28 +1,192 @@ -transcript_id consequence start end annotation gene -ENST00000375687.10 1720 4626 Hotspot ASXL1 -ENST00000498907.3 814 1077 Hotspot CEBPA -ENST00000321117.10 2644 2646 Hotspot DNMT3A -ENST00000320356.7 280 477 Hotspot EZH2 -ENST00000320356.7 652 999 Hotspot EZH2 -ENST00000320356.7 1507 1851 Hotspot EZH2 -ENST00000320356.7 1852 2253 Hotspot EZH2 -ENST00000241453.12 2503 2508 Hotspot FLT3 -ENST00000345146.7 394 396 Hotspot IDH1 -ENST00000330062.8 418 420 Hotspot IDH2 -ENST00000330062.8 514 516 Hotspot IDH2 -ENST00000288135.6 1246 1257 Hotspot KIT -ENST00000288135.6 2446 2448 Hotspot KIT -ENST00000296930.10 862 864 Hotspot NPM1 -ENST00000369535.5 34 39 Hotspot NRAS -ENST00000369535.5 181 183 Hotspot NRAS -ENST00000675419.1 229 612 Hotspot RUNX1 -ENST00000335508.11 1720 2370 Hotspot SF3B1 -ENST00000359995.10 283 285 Hotspot SRSF2 -ENST00000371145.8 646 648 Hotspot STAG2 -ENST00000380013.9 3310 4443 Hotspot TET2 -ENST00000380013.9 5527 6009 Hotspot TET2 -ENST00000269305.9 742 744 Hotspot TP53 -ENST00000291552.9 100 102 Hotspot U2AF1 -ENST00000291552.9 469 471 Hotspot U2AF1 -ENST00000452863.10 1114 1263 Hotspot WT1 -ENST00000452863.10 1357 1446 Hotspot WT1 +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 +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 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 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 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 stop_gained pathogenic +EZH2 ENST00000320356.7 stop_lost 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) +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 +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 +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 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 +ZRSR2 ENST00000307771.8 stop_lost pathogenic +ZRSR2 ENST00000307771.8 splice_acceptor_variant pathogenic +ZRSR2 ENST00000307771.8 splice_donor_variant pathogenic +TP53 ENST00000269305.9 frameshift_variant pathogenic +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 inframe_insertion possible pathogenic +TP53 ENST00000269305.9 inframe_deletion 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 +DDX41 ENST00000330503.12 missense_variant 1291 1701 likely 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 +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 stop_gained possible pathogenic +DNMT3A ENST00000321117.10 stop_lost possible pathogenic +ETNK1 ENST00000671733.1 missense_variant 727 734 (only known 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 +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 +IDH2 ENST00000330062.8 missense_variant 418 420 pathogenic +IDH2 ENST00000330062.8 missense_variant 514 516 pathogenic +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 +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 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 +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 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 +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) +UBA1 ENST00000335972.11 discard (only known pathogenic) +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 missense_variant 1357 1446 possible 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 From 82a66a63a3cc82ead0bd90c3f15275b19abd6ae6 Mon Sep 17 00:00:00 2001 From: acvandergrinten Date: Tue, 7 Oct 2025 09:30:01 +0200 Subject: [PATCH 2/5] annotation of AML known pathogenic variants --- utilities/deps/small-files/known_variants.tsv | 223 ++++++++++++++++++ 1 file changed, 223 insertions(+) create mode 100644 utilities/deps/small-files/known_variants.tsv diff --git a/utilities/deps/small-files/known_variants.tsv b/utilities/deps/small-files/known_variants.tsv new file mode 100644 index 00000000..ef06ef59 --- /dev/null +++ b/utilities/deps/small-files/known_variants.tsv @@ -0,0 +1,223 @@ +gene_name variant annotation +BRAF ENST00000646891.2:c.1781A>G known pathogenic +BRAF ENST00000646891.2:c.1799T>A known pathogenic +BRAF ENST00000646891.2:c.1799T>G known pathogenic +BRAF ENST00000646891.2:c.1801A>G known pathogenic +CALR ENST00000316448.10:c.1099_1150del known pathogenic (type 1) +CALR ENST00000316448.10:c.1100_1145del known pathogenic (type 1-like) +CALR ENST00000316448.10:c.1103_1136del known pathogenic (type 1-like) +CALR ENST00000316448.10:c.1154_1155insTTGTC known pathogenic (type 2) +CALR ENST00000316448.10:c.1155_1156insTGTCG known pathogenic (type 1-like) +CBL ENST00000264033.6:c.1096-1G>T known pathogenic +CBL ENST00000264033.6:c.1100A>C known pathogenic +CBL ENST00000264033.6:c.1111T>C known pathogenic +CBL ENST00000264033.6:c.1112A>G known pathogenic +CBL ENST00000264033.6:c.1144A>G known pathogenic +CBL ENST00000264033.6:c.1168G>T known pathogenic +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 +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 +ETNK1 ENST00000671733.1:c.727C>T known pathogenic +ETNK1 ENST00000671733.1:c.730A>C known pathogenic +ETNK1 ENST00000671733.1:c.731A>G known pathogenic +ETNK1 ENST00000671733.1:c.731A>C known pathogenic +ETNK1 ENST00000671733.1:c.731A>T known pathogenic +ETNK1 ENST00000671733.1:c.732T>A known pathogenic +ETNK1 ENST00000671733.1:c.734G>A known pathogenic +ETNK1 ENST00000671733.1:c.734G>C known pathogenic +ETNK1 ENST00000671733.1:c.734G>T known pathogenic +EZH2 ENST00000320356.7:c.1876G>A known pathogenic +EZH2 ENST00000320356.7:c.1936T>A known pathogenic +EZH2 ENST00000320356.7:c.1936T>C known pathogenic +EZH2 ENST00000320356.7:c.1937A>C known pathogenic +EZH2 ENST00000320356.7:c.1937A>G known pathogenic +EZH2 ENST00000320356.7:c.1937A>T known pathogenic +EZH2 ENST00000320356.7:c.1991A>G known pathogenic +EZH2 ENST00000320356.7:c.2045C>G known pathogenic +EZH2 ENST00000320356.7:c.2050C>T known pathogenic +EZH2 ENST00000320356.7:c.2068C>T known pathogenic +EZH2 ENST00000320356.7:c.2069G>A known pathogenic +EZH2 ENST00000320356.7:c.2233G>A known pathogenic +FLT3 ENST00000241453.12:c.2503G>A known pathogenic (TKD) +FLT3 ENST00000241453.12:c.2503G>C known pathogenic (TKD) +FLT3 ENST00000241453.12:c.2503G>T known pathogenic (TKD) +FLT3 ENST00000241453.12:c.2503_2505del known pathogenic (TKD) +FLT3 ENST00000241453.12:c.2504A>C known pathogenic (TKD) +FLT3 ENST00000241453.12:c.2504A>T known pathogenic (TKD) +FLT3 ENST00000241453.12:c.2505T>A known pathogenic (TKD) +FLT3 ENST00000241453.12:c.2505T>G known pathogenic (TKD) +FLT3 ENST00000241453.12:c.2506A>C known pathogenic (TKD) +FLT3 ENST00000241453.12:c.2506A>G known pathogenic (TKD) +FLT3 ENST00000241453.12:c.2506A>T known pathogenic (TKD) +FLT3 ENST00000241453.12:c.2506_2507delinsCA known pathogenic (TKD) +FLT3 ENST00000241453.12:c.2506_2507delinsGA known pathogenic (TKD) +FLT3 ENST00000241453.12:c.2507T>G known pathogenic (TKD) +FLT3 ENST00000241453.12:c.2508C>G known pathogenic (TKD) +FLT3 ENST00000241453.12:c.2508_2510del known pathogenic (TKD) +FLT3 ENST00000241453.12:c.2516A>G known pathogenic (TKD) +FLT3 ENST00000241453.12:c.2520_2521insGGATCC known pathogenic (TKD) +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) +IDH2 ENST00000330062.8:c.418C>G known pathogenic +IDH2 ENST00000330062.8:c.418C>T known pathogenic +IDH2 ENST00000330062.8:c.419G>A known pathogenic +IDH2 ENST00000330062.8:c.419G>T known pathogenic +IDH2 ENST00000330062.8:c.515G>A known pathogenic +IDH2 ENST00000330062.8:c.515G>T known pathogenic +IDH2 ENST00000330062.8:c.516G>C known pathogenic +JAK2 ENST00000381652.4:c.1849G>T known pathogenic (V617F) +JAK2 ENST00000381652.4:c.1611_1616del known pathogenic +JAK2 ENST00000381652.4:c.1615_1616delinsTT known pathogenic +JAK2 ENST00000381652.4:c.1622_1627del known pathogenic +JAK2 ENST00000381652.4:c.1624_1629del known pathogenic +JAK2 ENST00000381652.4:c.1627_1632del known pathogenic +KIT ENST00000288135.6:c.1255_1257del known pathogenic +KIT ENST00000288135.6:c.2446G>C known pathogenic +KIT ENST00000288135.6:c.2446G>T known pathogenic +KIT ENST00000288135.6:c.2446_2447delinsAT known pathogenic +KIT ENST00000288135.6:c.2447A>T known pathogenic +KIT ENST00000288135.6:c.2459A>G known pathogenic +KIT ENST00000288135.6:c.2466T>A known pathogenic +KIT ENST00000288135.6:c.2466T>G known pathogenic +KRAS ENST00000256078.10:c.34G>A known pathogenic +KRAS ENST00000256078.10:c.34G>C known pathogenic +KRAS ENST00000256078.10:c.34G>T known pathogenic +KRAS ENST00000256078.10:c.35G>A known pathogenic +KRAS ENST00000256078.10:c.35G>C known pathogenic +KRAS ENST00000256078.10:c.35G>T known pathogenic +KRAS ENST00000256078.10:c.37G>C known pathogenic +KRAS ENST00000256078.10:c.37G>T known pathogenic +KRAS ENST00000256078.10:c.38G>A known pathogenic +KRAS ENST00000256078.10:c.38G>T known pathogenic +KRAS ENST00000256078.10:c.40G>A known pathogenic +KRAS ENST00000256078.10:c.173C>T known pathogenic +KRAS ENST00000256078.10:c.181C>A known pathogenic +KRAS ENST00000256078.10:c.181C>G known pathogenic +KRAS ENST00000256078.10:c.182A>G known pathogenic +KRAS ENST00000256078.10:c.182A>T known pathogenic +KRAS ENST00000256078.10:c.183A>C known pathogenic +KRAS ENST00000256078.10:c.183A>T known pathogenic +KRAS ENST00000256078.10:c.53C>A known pathogenic +KRAS ENST00000256078.10:c.68T>G known pathogenic +KRAS ENST00000256078.10:c.176C>A known pathogenic +KRAS ENST00000256078.10:c.179G>A known pathogenic +KRAS ENST00000256078.10:c.182A>C known pathogenic +KRAS ENST00000256078.10:c.190T>A known pathogenic +MPL ENST00000372470.9:c.1543T>A known pathogenic +MPL ENST00000372470.9:c.1543T>C known pathogenic +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.1514G>A known pathogenic +NFE2 ENST00000435572.7:c.782_785del known pathogenic +NPM1 ENST00000296930.10:c.860_863dup known pathogenic (type A) +NPM1 ENST00000296930.10:c.863_864insCATG known pathogenic (type B) +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) +NRAS ENST00000369535.5:c.34G>A known pathogenic +NRAS ENST00000369535.5:c.34G>C known pathogenic +NRAS ENST00000369535.5:c.34G>T known pathogenic +NRAS ENST00000369535.5:c.34_35delinsAT known pathogenic +NRAS ENST00000369535.5:c.35G>A known pathogenic +NRAS ENST00000369535.5:c.35G>C known pathogenic +NRAS ENST00000369535.5:c.35G>T known pathogenic +NRAS ENST00000369535.5:c.37G>C known pathogenic +NRAS ENST00000369535.5:c.38G>A known pathogenic +NRAS ENST00000369535.5:c.38G>T known pathogenic +NRAS ENST00000369535.5:c.181C>A known pathogenic +NRAS ENST00000369535.5:c.182A>C known pathogenic +NRAS ENST00000369535.5:c.182A>G known pathogenic +NRAS ENST00000369535.5:c.182A>T known pathogenic +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.602G>A 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 +RUNX1 ENST00000675419.1:c.320G>A known pathogenic +RUNX1 ENST00000675419.1:c.320G>C known pathogenic +RUNX1 ENST00000675419.1:c.422C>T known pathogenic +RUNX1 ENST00000675419.1:c.485G>A known pathogenic +RUNX1 ENST00000675419.1:c.496C>G known pathogenic +RUNX1 ENST00000675419.1:c.497G>A known pathogenic +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.611G>T known pathogenic +RUNX1 ENST00000675419.1:c.619C>T known pathogenic +RUNX1 ENST00000675419.1:c.620G>A 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 +SETBP1 ENST00000649279.2:c.2609G>A known pathogenic +SETBP1 ENST00000649279.2:c.2612T>C known pathogenic +SF3B1 ENST00000335508.11:c.1866G>C known pathogenic +SF3B1 ENST00000335508.11:c.1866G>T known pathogenic +SF3B1 ENST00000335508.11:c.1868A>G known pathogenic +SF3B1 ENST00000335508.11:c.1873C>G known pathogenic +SF3B1 ENST00000335508.11:c.1873C>T known pathogenic +SF3B1 ENST00000335508.11:c.1874G>T known pathogenic +SF3B1 ENST00000335508.11:c.1876A>G known pathogenic +SF3B1 ENST00000335508.11:c.1972T>C known pathogenic +SF3B1 ENST00000335508.11:c.1984C>G known pathogenic +SF3B1 ENST00000335508.11:c.1986C>A known pathogenic +SF3B1 ENST00000335508.11:c.1986C>G known pathogenic +SF3B1 ENST00000335508.11:c.1996A>C known pathogenic +SF3B1 ENST00000335508.11:c.1996A>G known pathogenic +SF3B1 ENST00000335508.11:c.1997A>C known pathogenic +SF3B1 ENST00000335508.11:c.1997A>G known pathogenic +SF3B1 ENST00000335508.11:c.1997A>T known pathogenic +SF3B1 ENST00000335508.11:c.1998G>C known pathogenic +SF3B1 ENST00000335508.11:c.1998G>T known pathogenic +SF3B1 ENST00000335508.11:c.2094_2098delinsACAGG known pathogenic +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.287C>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.5618T>C known pathogenic +TP53 ENST00000269305.9:c.524G>A known pathogenic +TP53 ENST00000269305.9:c.536A>G known pathogenic +TP53 ENST00000269305.9:c.659A>G known pathogenic +TP53 ENST00000269305.9:c.673-1G>T known pathogenic +TP53 ENST00000269305.9:c.734G>T known pathogenic +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.488A>G known pathogenic +TP53 ENST00000269305.9:c.559+1G>A known pathogenic +TP53 ENST00000269305.9:c.658T>C known pathogenic +TP53 ENST00000269305.9:c.701A>G known pathogenic +TP53 ENST00000269305.9:c.817C>T known pathogenic +U2AF1 ENST00000291552.9:c.101C>A known pathogenic +U2AF1 ENST00000291552.9:c.101C>T known pathogenic +U2AF1 ENST00000291552.9:c.467G>A known pathogenic +U2AF1 ENST00000291552.9:c.470A>C known pathogenic +U2AF1 ENST00000291552.9:c.470A>G known pathogenic +U2AF1 ENST00000291552.9:c.471G>C known pathogenic +UBA1 ENST00000335972.11:c.121A>C known pathogenic (VEXAS) +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.1399C>T known pathogenic +WT1 ENST00000452863.10:c.1400G>C known pathogenic +WT1 ENST00000452863.10:c.1153C>G known pathogenic \ No newline at end of file From ca894b7a955f6b99587c4f2c180e525740ee2cf1 Mon Sep 17 00:00:00 2001 From: acvandergrinten Date: Wed, 8 Oct 2025 15:22:46 +0200 Subject: [PATCH 3/5] assume known_variants file has column names --- docs/source/snv-indels.rst | 3 +++ includes/snv-indels/scripts/annotate_vep.py | 23 ++++++++++++++++++++- 2 files changed, 25 insertions(+), 1 deletion(-) diff --git a/docs/source/snv-indels.rst b/docs/source/snv-indels.rst index 74404677..628a3d87 100644 --- a/docs/source/snv-indels.rst +++ b/docs/source/snv-indels.rst @@ -130,6 +130,9 @@ supply HAMLET with annotations for specific variants via the ``known_variants`` file. Annotations from this file have a higher priority than the annotations specified in ``annotation_criteria``. +The used columns are ``variant`` and ``annotation``. In case ``annotation`` is +empty, the annotation is set to ``known pathogenic``. + .. csv-table:: Example ``known_variants`` file, from the HAMLET tests :delim: U+0009 :file: ../../test/data/config/known_variants.tsv diff --git a/includes/snv-indels/scripts/annotate_vep.py b/includes/snv-indels/scripts/annotate_vep.py index ba7cf8e0..029c9ad9 100644 --- a/includes/snv-indels/scripts/annotate_vep.py +++ b/includes/snv-indels/scripts/annotate_vep.py @@ -3,6 +3,7 @@ import argparse import json from utils import Variant, VEP, read_criteria_file +from itertools import zip_longest from typing import Iterator @@ -15,9 +16,29 @@ def parse_vep_json(vep_file: str) -> Iterator[VEP]: def read_known_variants(fname: str) -> dict[str, str]: known_variants = dict() + header = None with open(fname) as fin: for line in fin: - variant, annotation = line.strip("\n").split("\t") + if line.startswith("#"): + continue + + spline = line.strip("\n").split("\t") + if header is None: + header = spline + continue + + # Read into dict, convert '' to None + d = {k: v if v else None for k, v in zip_longest(header, spline)} + + # Check that the variant column is filled + variant = d.get("variant") + assert variant is not None + + # If there is no annotation specified, use annotation "known pathogenic" + annotation = d.get("annotation") + if annotation is None: + annotation = "known pathogenic" + known_variants[variant] = annotation return known_variants From b989d1d94d571a7b052f012b0d1fec0a32fbf96b Mon Sep 17 00:00:00 2001 From: acvandergrinten Date: Thu, 9 Oct 2025 12:00:26 +0200 Subject: [PATCH 4/5] removed default so annotation col cannot be empty --- docs/source/snv-indels.rst | 4 ++-- includes/snv-indels/scripts/annotate_vep.py | 5 ++--- 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/docs/source/snv-indels.rst b/docs/source/snv-indels.rst index 628a3d87..df086b44 100644 --- a/docs/source/snv-indels.rst +++ b/docs/source/snv-indels.rst @@ -130,8 +130,8 @@ supply HAMLET with annotations for specific variants via the ``known_variants`` file. Annotations from this file have a higher priority than the annotations specified in ``annotation_criteria``. -The used columns are ``variant`` and ``annotation``. In case ``annotation`` is -empty, the annotation is set to ``known pathogenic``. +The used columns are ``variant`` and ``annotation``. These columns cannot be +empty. .. csv-table:: Example ``known_variants`` file, from the HAMLET tests :delim: U+0009 diff --git a/includes/snv-indels/scripts/annotate_vep.py b/includes/snv-indels/scripts/annotate_vep.py index 029c9ad9..9f117b88 100644 --- a/includes/snv-indels/scripts/annotate_vep.py +++ b/includes/snv-indels/scripts/annotate_vep.py @@ -34,10 +34,9 @@ def read_known_variants(fname: str) -> dict[str, str]: variant = d.get("variant") assert variant is not None - # If there is no annotation specified, use annotation "known pathogenic" + # Check that the annotation column is filled annotation = d.get("annotation") - if annotation is None: - annotation = "known pathogenic" + assert annotation is not None known_variants[variant] = annotation return known_variants From e8e1a3edcae8d1575e0537904c02e45553001a68 Mon Sep 17 00:00:00 2001 From: acvandergrinten Date: Thu, 23 Oct 2025 13:15:08 +0200 Subject: [PATCH 5/5] small fixes in criteria after containment check --- .../deps/small-files/annotation_criteria.tsv | 12 +- .../deps/small-files/filter_criteria.tsv | 394 ---------------- .../deps/small-files/inclusion_criteria.tsv | 441 ++++++++++++++++++ 3 files changed, 447 insertions(+), 400 deletions(-) delete mode 100644 utilities/deps/small-files/filter_criteria.tsv create mode 100644 utilities/deps/small-files/inclusion_criteria.tsv diff --git a/utilities/deps/small-files/annotation_criteria.tsv b/utilities/deps/small-files/annotation_criteria.tsv index 0ac5fffc..26e6d79a 100644 --- a/utilities/deps/small-files/annotation_criteria.tsv +++ b/utilities/deps/small-files/annotation_criteria.tsv @@ -26,7 +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 @@ -73,7 +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) @@ -120,7 +120,7 @@ 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) @@ -175,8 +175,8 @@ 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 @@ -189,4 +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 diff --git a/utilities/deps/small-files/filter_criteria.tsv b/utilities/deps/small-files/filter_criteria.tsv deleted file mode 100644 index 6962f353..00000000 --- a/utilities/deps/small-files/filter_criteria.tsv +++ /dev/null @@ -1,394 +0,0 @@ -gene_name transcript_id consequence start end frame annotation -ASXL1 ENST00000375687.10 stop_gained -ASXL1 ENST00000375687.10 frameshift_variant -ASXL1 ENST00000375687.10 stop_lost -ASXL1 ENST00000375687.10 start_lost -ASXL1 ENST00000375687.10 inframe_insertion -ASXL1 ENST00000375687.10 inframe_deletion -ASXL1 ENST00000375687.10 protein_altering_variant -ASXL1 ENST00000375687.10 missense_variant -CEBPA ENST00000498907.3 stop_gained -CEBPA ENST00000498907.3 frameshift_variant -CEBPA ENST00000498907.3 stop_lost -CEBPA ENST00000498907.3 start_lost -CEBPA ENST00000498907.3 inframe_insertion -CEBPA ENST00000498907.3 inframe_deletion -CEBPA ENST00000498907.3 protein_altering_variant -CEBPA ENST00000498907.3 missense_variant -DNMT3A ENST00000321117.10 stop_gained -DNMT3A ENST00000321117.10 frameshift_variant -DNMT3A ENST00000321117.10 stop_lost -DNMT3A ENST00000321117.10 start_lost -DNMT3A ENST00000321117.10 inframe_insertion -DNMT3A ENST00000321117.10 inframe_deletion -DNMT3A ENST00000321117.10 protein_altering_variant -DNMT3A ENST00000321117.10 missense_variant -FLT3 ENST00000241453.12 stop_gained -FLT3 ENST00000241453.12 frameshift_variant -FLT3 ENST00000241453.12 stop_lost -FLT3 ENST00000241453.12 start_lost -FLT3 ENST00000241453.12 inframe_insertion -FLT3 ENST00000241453.12 inframe_deletion -FLT3 ENST00000241453.12 protein_altering_variant -FLT3 ENST00000241453.12 missense_variant -IDH1 ENST00000345146.7 stop_gained -IDH1 ENST00000345146.7 frameshift_variant -IDH1 ENST00000345146.7 stop_lost -IDH1 ENST00000345146.7 start_lost -IDH1 ENST00000345146.7 inframe_insertion -IDH1 ENST00000345146.7 inframe_deletion -IDH1 ENST00000345146.7 protein_altering_variant -IDH1 ENST00000345146.7 missense_variant -IDH2 ENST00000330062.8 stop_gained -IDH2 ENST00000330062.8 frameshift_variant -IDH2 ENST00000330062.8 stop_lost -IDH2 ENST00000330062.8 start_lost -IDH2 ENST00000330062.8 inframe_insertion -IDH2 ENST00000330062.8 inframe_deletion -IDH2 ENST00000330062.8 protein_altering_variant -IDH2 ENST00000330062.8 missense_variant -KIT ENST00000288135.6 stop_gained -KIT ENST00000288135.6 frameshift_variant -KIT ENST00000288135.6 stop_lost -KIT ENST00000288135.6 start_lost -KIT ENST00000288135.6 inframe_insertion -KIT ENST00000288135.6 inframe_deletion -KIT ENST00000288135.6 protein_altering_variant -KIT ENST00000288135.6 missense_variant -NPM1 ENST00000296930.10 stop_gained -NPM1 ENST00000296930.10 frameshift_variant -NPM1 ENST00000296930.10 stop_lost -NPM1 ENST00000296930.10 start_lost -NPM1 ENST00000296930.10 inframe_insertion -NPM1 ENST00000296930.10 inframe_deletion -NPM1 ENST00000296930.10 protein_altering_variant -NPM1 ENST00000296930.10 missense_variant -NRAS ENST00000369535.5 stop_gained -NRAS ENST00000369535.5 frameshift_variant -NRAS ENST00000369535.5 stop_lost -NRAS ENST00000369535.5 start_lost -NRAS ENST00000369535.5 inframe_insertion -NRAS ENST00000369535.5 inframe_deletion -NRAS ENST00000369535.5 protein_altering_variant -NRAS ENST00000369535.5 missense_variant -RUNX1 ENST00000675419.1 stop_gained -RUNX1 ENST00000675419.1 frameshift_variant -RUNX1 ENST00000675419.1 stop_lost -RUNX1 ENST00000675419.1 start_lost -RUNX1 ENST00000675419.1 inframe_insertion -RUNX1 ENST00000675419.1 inframe_deletion -RUNX1 ENST00000675419.1 protein_altering_variant -RUNX1 ENST00000675419.1 missense_variant -TET2 ENST00000380013.9 stop_gained -TET2 ENST00000380013.9 frameshift_variant -TET2 ENST00000380013.9 stop_lost -TET2 ENST00000380013.9 start_lost -TET2 ENST00000380013.9 inframe_insertion -TET2 ENST00000380013.9 inframe_deletion -TET2 ENST00000380013.9 protein_altering_variant -TET2 ENST00000380013.9 missense_variant -TP53 ENST00000269305.9 stop_gained -TP53 ENST00000269305.9 frameshift_variant -TP53 ENST00000269305.9 stop_lost -TP53 ENST00000269305.9 start_lost -TP53 ENST00000269305.9 inframe_insertion -TP53 ENST00000269305.9 inframe_deletion -TP53 ENST00000269305.9 protein_altering_variant -TP53 ENST00000269305.9 missense_variant -WT1 ENST00000452863.10 stop_gained -WT1 ENST00000452863.10 frameshift_variant -WT1 ENST00000452863.10 stop_lost -WT1 ENST00000452863.10 start_lost -WT1 ENST00000452863.10 inframe_insertion -WT1 ENST00000452863.10 inframe_deletion -WT1 ENST00000452863.10 protein_altering_variant -WT1 ENST00000452863.10 missense_variant -SRSF2 ENST00000359995.10 stop_gained -SRSF2 ENST00000359995.10 frameshift_variant -SRSF2 ENST00000359995.10 stop_lost -SRSF2 ENST00000359995.10 start_lost -SRSF2 ENST00000359995.10 inframe_insertion -SRSF2 ENST00000359995.10 inframe_deletion -SRSF2 ENST00000359995.10 protein_altering_variant -SRSF2 ENST00000359995.10 missense_variant -SF3B1 ENST00000335508.11 stop_gained -SF3B1 ENST00000335508.11 frameshift_variant -SF3B1 ENST00000335508.11 stop_lost -SF3B1 ENST00000335508.11 start_lost -SF3B1 ENST00000335508.11 inframe_insertion -SF3B1 ENST00000335508.11 inframe_deletion -SF3B1 ENST00000335508.11 protein_altering_variant -SF3B1 ENST00000335508.11 missense_variant -U2AF1 ENST00000291552.9 stop_gained -U2AF1 ENST00000291552.9 frameshift_variant -U2AF1 ENST00000291552.9 stop_lost -U2AF1 ENST00000291552.9 start_lost -U2AF1 ENST00000291552.9 inframe_insertion -U2AF1 ENST00000291552.9 inframe_deletion -U2AF1 ENST00000291552.9 protein_altering_variant -U2AF1 ENST00000291552.9 missense_variant -BCOR ENST00000378444.9 stop_gained -BCOR ENST00000378444.9 frameshift_variant -BCOR ENST00000378444.9 stop_lost -BCOR ENST00000378444.9 start_lost -BCOR ENST00000378444.9 inframe_insertion -BCOR ENST00000378444.9 inframe_deletion -BCOR ENST00000378444.9 protein_altering_variant -BCOR ENST00000378444.9 missense_variant -STAG2 ENST00000371145.8 stop_gained -STAG2 ENST00000371145.8 frameshift_variant -STAG2 ENST00000371145.8 stop_lost -STAG2 ENST00000371145.8 start_lost -STAG2 ENST00000371145.8 inframe_insertion -STAG2 ENST00000371145.8 inframe_deletion -STAG2 ENST00000371145.8 protein_altering_variant -STAG2 ENST00000371145.8 missense_variant -ZRSR2 ENST00000307771.8 stop_gained -ZRSR2 ENST00000307771.8 frameshift_variant -ZRSR2 ENST00000307771.8 stop_lost -ZRSR2 ENST00000307771.8 start_lost -ZRSR2 ENST00000307771.8 inframe_insertion -ZRSR2 ENST00000307771.8 inframe_deletion -ZRSR2 ENST00000307771.8 protein_altering_variant -ZRSR2 ENST00000307771.8 missense_variant -EZH2 ENST00000320356.7 stop_gained -EZH2 ENST00000320356.7 frameshift_variant -EZH2 ENST00000320356.7 stop_lost -EZH2 ENST00000320356.7 start_lost -EZH2 ENST00000320356.7 inframe_insertion -EZH2 ENST00000320356.7 inframe_deletion -EZH2 ENST00000320356.7 protein_altering_variant -EZH2 ENST00000320356.7 missense_variant -BCORL1 ENST00000540052.6 stop_gained -BCORL1 ENST00000540052.6 frameshift_variant -BCORL1 ENST00000540052.6 stop_lost -BCORL1 ENST00000540052.6 start_lost -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 -BRAF ENST00000646891.2 start_lost -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 -CALR ENST00000316448.10 start_lost -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 -CBL ENST00000264033.6 start_lost -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 -CSF3R ENST00000373103.5 start_lost -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 -CUX1 ENST00000292535.12 start_lost -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 -DDX41 ENST00000330503.12 start_lost -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 -ETNK1 ENST00000671733.1 start_lost -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 -ETV6 ENST00000396373.9 start_lost -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 -GATA2 ENST00000341105.7 start_lost -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 -GNB1 ENST00000378609.9 start_lost -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 -JAK2 ENST00000381652.4 start_lost -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 -KRAS ENST00000256078.10 start_lost -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 -MYC ENST00000621592.8 start_lost -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 -NF1 ENST00000358273.9 start_lost -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 -NFE2 ENST00000435572.7 start_lost -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 -PHF6 ENST00000332070.7 start_lost -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 -PPM1D ENST00000305921.8 start_lost -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 -PRPF8 ENST00000304992.11 start_lost -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 -PTPN11 ENST00000351677.7 start_lost -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 -RAD21 ENST00000297338.7 start_lost -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 -SETBP1 ENST00000649279.2 stop_gained -SETBP1 ENST00000649279.2 frameshift_variant -SETBP1 ENST00000649279.2 stop_lost -SETBP1 ENST00000649279.2 start_lost -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 -UBA1 ENST00000335972.11 frameshift_variant -UBA1 ENST00000335972.11 stop_lost -UBA1 ENST00000335972.11 start_lost -UBA1 ENST00000335972.11 inframe_insertion -UBA1 ENST00000335972.11 inframe_deletion -UBA1 ENST00000335972.11 protein_altering_variant -UBA1 ENST00000335972.11 missense_variant -UBA1 ENST00000335972.11 stop_gained diff --git a/utilities/deps/small-files/inclusion_criteria.tsv b/utilities/deps/small-files/inclusion_criteria.tsv new file mode 100644 index 00000000..8c11a7f9 --- /dev/null +++ b/utilities/deps/small-files/inclusion_criteria.tsv @@ -0,0 +1,441 @@ +gene_name transcript_id consequence start end +ASXL1 ENST00000375687.10 frameshift_variant +ASXL1 ENST00000375687.10 inframe_deletion +ASXL1 ENST00000375687.10 inframe_insertion +ASXL1 ENST00000375687.10 missense_variant +ASXL1 ENST00000375687.10 protein_altering_variant +ASXL1 ENST00000375687.10 splice_acceptor_variant +ASXL1 ENST00000375687.10 splice_donor_variant +ASXL1 ENST00000375687.10 start_lost +ASXL1 ENST00000375687.10 stop_gained +ASXL1 ENST00000375687.10 stop_lost +BCOR ENST00000378444.9 frameshift_variant +BCOR ENST00000378444.9 inframe_deletion +BCOR ENST00000378444.9 inframe_insertion +BCOR ENST00000378444.9 missense_variant +BCOR ENST00000378444.9 protein_altering_variant +BCOR ENST00000378444.9 splice_acceptor_variant +BCOR ENST00000378444.9 splice_donor_variant +BCOR ENST00000378444.9 start_lost +BCOR ENST00000378444.9 stop_gained +BCOR ENST00000378444.9 stop_lost +BCORL1 ENST00000540052.6 frameshift_variant +BCORL1 ENST00000540052.6 inframe_deletion +BCORL1 ENST00000540052.6 inframe_insertion +BCORL1 ENST00000540052.6 missense_variant +BCORL1 ENST00000540052.6 protein_altering_variant +BCORL1 ENST00000540052.6 splice_acceptor_variant +BCORL1 ENST00000540052.6 splice_donor_variant +BCORL1 ENST00000540052.6 start_lost +BCORL1 ENST00000540052.6 stop_gained +BCORL1 ENST00000540052.6 stop_lost +BRAF ENST00000646891.2 frameshift_variant +BRAF ENST00000646891.2 inframe_deletion +BRAF ENST00000646891.2 inframe_insertion +BRAF ENST00000646891.2 missense_variant +BRAF ENST00000646891.2 protein_altering_variant +BRAF ENST00000646891.2 splice_acceptor_variant +BRAF ENST00000646891.2 splice_donor_variant +BRAF ENST00000646891.2 start_lost +BRAF ENST00000646891.2 stop_gained +BRAF ENST00000646891.2 stop_lost +CALR ENST00000316448.10 frameshift_variant +CALR ENST00000316448.10 inframe_deletion +CALR ENST00000316448.10 inframe_insertion +CALR ENST00000316448.10 missense_variant +CALR ENST00000316448.10 protein_altering_variant +CALR ENST00000316448.10 splice_acceptor_variant +CALR ENST00000316448.10 splice_donor_variant +CALR ENST00000316448.10 start_lost +CALR ENST00000316448.10 stop_gained +CALR ENST00000316448.10 stop_lost +CBL ENST00000264033.6 frameshift_variant +CBL ENST00000264033.6 inframe_deletion +CBL ENST00000264033.6 inframe_insertion +CBL ENST00000264033.6 missense_variant +CBL ENST00000264033.6 protein_altering_variant +CBL ENST00000264033.6 splice_acceptor_variant +CBL ENST00000264033.6 splice_donor_variant +CBL ENST00000264033.6 start_lost +CBL ENST00000264033.6 stop_gained +CBL ENST00000264033.6 stop_lost +CEBPA ENST00000498907.3 frameshift_variant +CEBPA ENST00000498907.3 inframe_deletion +CEBPA ENST00000498907.3 inframe_insertion +CEBPA ENST00000498907.3 missense_variant +CEBPA ENST00000498907.3 protein_altering_variant +CEBPA ENST00000498907.3 splice_acceptor_variant +CEBPA ENST00000498907.3 splice_donor_variant +CEBPA ENST00000498907.3 start_lost +CEBPA ENST00000498907.3 stop_gained +CEBPA ENST00000498907.3 stop_lost +CSF3R ENST00000373103.5 frameshift_variant +CSF3R ENST00000373103.5 inframe_deletion +CSF3R ENST00000373103.5 inframe_insertion +CSF3R ENST00000373103.5 missense_variant +CSF3R ENST00000373103.5 protein_altering_variant +CSF3R ENST00000373103.5 splice_acceptor_variant +CSF3R ENST00000373103.5 splice_donor_variant +CSF3R ENST00000373103.5 start_lost +CSF3R ENST00000373103.5 stop_gained +CSF3R ENST00000373103.5 stop_lost +DDX41 ENST00000330503.12 frameshift_variant +DDX41 ENST00000330503.12 inframe_deletion +DDX41 ENST00000330503.12 inframe_insertion +DDX41 ENST00000330503.12 missense_variant +DDX41 ENST00000330503.12 protein_altering_variant +DDX41 ENST00000330503.12 splice_acceptor_variant +DDX41 ENST00000330503.12 splice_donor_variant +DDX41 ENST00000330503.12 start_lost +DDX41 ENST00000330503.12 stop_gained +DDX41 ENST00000330503.12 stop_lost +DNMT3A ENST00000321117.10 frameshift_variant +DNMT3A ENST00000321117.10 inframe_deletion +DNMT3A ENST00000321117.10 inframe_insertion +DNMT3A ENST00000321117.10 missense_variant +DNMT3A ENST00000321117.10 protein_altering_variant +DNMT3A ENST00000321117.10 splice_acceptor_variant +DNMT3A ENST00000321117.10 splice_donor_variant +DNMT3A ENST00000321117.10 start_lost +DNMT3A ENST00000321117.10 stop_gained +DNMT3A ENST00000321117.10 stop_lost +ETNK1 ENST00000671733.1 frameshift_variant +ETNK1 ENST00000671733.1 inframe_deletion +ETNK1 ENST00000671733.1 inframe_insertion +ETNK1 ENST00000671733.1 missense_variant +ETNK1 ENST00000671733.1 protein_altering_variant +ETNK1 ENST00000671733.1 splice_acceptor_variant +ETNK1 ENST00000671733.1 splice_donor_variant +ETNK1 ENST00000671733.1 start_lost +ETNK1 ENST00000671733.1 stop_gained +ETNK1 ENST00000671733.1 stop_lost +ETV6 ENST00000396373.9 frameshift_variant +ETV6 ENST00000396373.9 inframe_deletion +ETV6 ENST00000396373.9 inframe_insertion +ETV6 ENST00000396373.9 missense_variant +ETV6 ENST00000396373.9 protein_altering_variant +ETV6 ENST00000396373.9 splice_acceptor_variant +ETV6 ENST00000396373.9 splice_donor_variant +ETV6 ENST00000396373.9 start_lost +ETV6 ENST00000396373.9 stop_gained +ETV6 ENST00000396373.9 stop_lost +EZH2 ENST00000320356.7 frameshift_variant +EZH2 ENST00000320356.7 inframe_deletion +EZH2 ENST00000320356.7 inframe_insertion +EZH2 ENST00000320356.7 missense_variant +EZH2 ENST00000320356.7 protein_altering_variant +EZH2 ENST00000320356.7 splice_acceptor_variant +EZH2 ENST00000320356.7 splice_donor_variant +EZH2 ENST00000320356.7 start_lost +EZH2 ENST00000320356.7 stop_gained +EZH2 ENST00000320356.7 stop_lost +FLT3 ENST00000241453.12 frameshift_variant +FLT3 ENST00000241453.12 inframe_deletion +FLT3 ENST00000241453.12 inframe_insertion +FLT3 ENST00000241453.12 missense_variant +FLT3 ENST00000241453.12 protein_altering_variant +FLT3 ENST00000241453.12 splice_acceptor_variant +FLT3 ENST00000241453.12 splice_donor_variant +FLT3 ENST00000241453.12 start_lost +FLT3 ENST00000241453.12 stop_gained +FLT3 ENST00000241453.12 stop_lost +GATA2 ENST00000341105.7 frameshift_variant +GATA2 ENST00000341105.7 inframe_deletion +GATA2 ENST00000341105.7 inframe_insertion +GATA2 ENST00000341105.7 missense_variant +GATA2 ENST00000341105.7 protein_altering_variant +GATA2 ENST00000341105.7 splice_acceptor_variant +GATA2 ENST00000341105.7 splice_donor_variant +GATA2 ENST00000341105.7 start_lost +GATA2 ENST00000341105.7 stop_gained +GATA2 ENST00000341105.7 stop_lost +GNB1 ENST00000378609.9 frameshift_variant +GNB1 ENST00000378609.9 inframe_deletion +GNB1 ENST00000378609.9 inframe_insertion +GNB1 ENST00000378609.9 missense_variant +GNB1 ENST00000378609.9 protein_altering_variant +GNB1 ENST00000378609.9 splice_acceptor_variant +GNB1 ENST00000378609.9 splice_donor_variant +GNB1 ENST00000378609.9 start_lost +GNB1 ENST00000378609.9 stop_gained +GNB1 ENST00000378609.9 stop_lost +IDH1 ENST00000345146.7 frameshift_variant +IDH1 ENST00000345146.7 inframe_deletion +IDH1 ENST00000345146.7 inframe_insertion +IDH1 ENST00000345146.7 missense_variant +IDH1 ENST00000345146.7 protein_altering_variant +IDH1 ENST00000345146.7 splice_acceptor_variant +IDH1 ENST00000345146.7 splice_donor_variant +IDH1 ENST00000345146.7 start_lost +IDH1 ENST00000345146.7 stop_gained +IDH1 ENST00000345146.7 stop_lost +IDH2 ENST00000330062.8 frameshift_variant +IDH2 ENST00000330062.8 inframe_deletion +IDH2 ENST00000330062.8 inframe_insertion +IDH2 ENST00000330062.8 missense_variant +IDH2 ENST00000330062.8 protein_altering_variant +IDH2 ENST00000330062.8 splice_acceptor_variant +IDH2 ENST00000330062.8 splice_donor_variant +IDH2 ENST00000330062.8 start_lost +IDH2 ENST00000330062.8 stop_gained +IDH2 ENST00000330062.8 stop_lost +JAK2 ENST00000381652.4 frameshift_variant +JAK2 ENST00000381652.4 inframe_deletion +JAK2 ENST00000381652.4 inframe_insertion +JAK2 ENST00000381652.4 missense_variant +JAK2 ENST00000381652.4 protein_altering_variant +JAK2 ENST00000381652.4 splice_acceptor_variant +JAK2 ENST00000381652.4 splice_donor_variant +JAK2 ENST00000381652.4 start_lost +JAK2 ENST00000381652.4 stop_gained +JAK2 ENST00000381652.4 stop_lost +KIT ENST00000288135.6 frameshift_variant +KIT ENST00000288135.6 inframe_deletion +KIT ENST00000288135.6 inframe_insertion +KIT ENST00000288135.6 missense_variant +KIT ENST00000288135.6 protein_altering_variant +KIT ENST00000288135.6 splice_acceptor_variant +KIT ENST00000288135.6 splice_donor_variant +KIT ENST00000288135.6 start_lost +KIT ENST00000288135.6 stop_gained +KIT ENST00000288135.6 stop_lost +KRAS ENST00000256078.10 frameshift_variant +KRAS ENST00000256078.10 inframe_deletion +KRAS ENST00000256078.10 inframe_insertion +KRAS ENST00000256078.10 missense_variant +KRAS ENST00000256078.10 protein_altering_variant +KRAS ENST00000256078.10 splice_acceptor_variant +KRAS ENST00000256078.10 splice_donor_variant +KRAS ENST00000256078.10 start_lost +KRAS ENST00000256078.10 stop_gained +KRAS ENST00000256078.10 stop_lost +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 splice_acceptor_variant +MPL ENST00000372470.9 splice_donor_variant +MPL ENST00000372470.9 start_lost +MPL ENST00000372470.9 stop_gained +MPL ENST00000372470.9 stop_lost +NF1 ENST00000358273.9 frameshift_variant +NF1 ENST00000358273.9 inframe_deletion +NF1 ENST00000358273.9 inframe_insertion +NF1 ENST00000358273.9 missense_variant +NF1 ENST00000358273.9 protein_altering_variant +NF1 ENST00000358273.9 splice_acceptor_variant +NF1 ENST00000358273.9 splice_donor_variant +NF1 ENST00000358273.9 start_lost +NF1 ENST00000358273.9 stop_gained +NF1 ENST00000358273.9 stop_lost +NFE2 ENST00000435572.7 frameshift_variant +NFE2 ENST00000435572.7 inframe_deletion +NFE2 ENST00000435572.7 inframe_insertion +NFE2 ENST00000435572.7 missense_variant +NFE2 ENST00000435572.7 protein_altering_variant +NFE2 ENST00000435572.7 splice_acceptor_variant +NFE2 ENST00000435572.7 splice_donor_variant +NFE2 ENST00000435572.7 start_lost +NFE2 ENST00000435572.7 stop_gained +NFE2 ENST00000435572.7 stop_lost +NPM1 ENST00000296930.10 frameshift_variant +NPM1 ENST00000296930.10 inframe_deletion +NPM1 ENST00000296930.10 inframe_insertion +NPM1 ENST00000296930.10 missense_variant +NPM1 ENST00000296930.10 protein_altering_variant +NPM1 ENST00000296930.10 splice_acceptor_variant +NPM1 ENST00000296930.10 splice_donor_variant +NPM1 ENST00000296930.10 start_lost +NPM1 ENST00000296930.10 stop_gained +NPM1 ENST00000296930.10 stop_lost +NRAS ENST00000369535.5 frameshift_variant +NRAS ENST00000369535.5 inframe_deletion +NRAS ENST00000369535.5 inframe_insertion +NRAS ENST00000369535.5 missense_variant +NRAS ENST00000369535.5 protein_altering_variant +NRAS ENST00000369535.5 splice_acceptor_variant +NRAS ENST00000369535.5 splice_donor_variant +NRAS ENST00000369535.5 start_lost +NRAS ENST00000369535.5 stop_gained +NRAS ENST00000369535.5 stop_lost +PHF6 ENST00000332070.7 frameshift_variant +PHF6 ENST00000332070.7 inframe_deletion +PHF6 ENST00000332070.7 inframe_insertion +PHF6 ENST00000332070.7 missense_variant +PHF6 ENST00000332070.7 protein_altering_variant +PHF6 ENST00000332070.7 splice_acceptor_variant +PHF6 ENST00000332070.7 splice_donor_variant +PHF6 ENST00000332070.7 start_lost +PHF6 ENST00000332070.7 stop_gained +PHF6 ENST00000332070.7 stop_lost +PPM1D ENST00000305921.8 frameshift_variant +PPM1D ENST00000305921.8 inframe_deletion +PPM1D ENST00000305921.8 inframe_insertion +PPM1D ENST00000305921.8 missense_variant +PPM1D ENST00000305921.8 protein_altering_variant +PPM1D ENST00000305921.8 splice_acceptor_variant +PPM1D ENST00000305921.8 splice_donor_variant +PPM1D ENST00000305921.8 start_lost +PPM1D ENST00000305921.8 stop_gained +PPM1D ENST00000305921.8 stop_lost +PRPF8 ENST00000304992.11 frameshift_variant +PRPF8 ENST00000304992.11 inframe_deletion +PRPF8 ENST00000304992.11 inframe_insertion +PRPF8 ENST00000304992.11 missense_variant +PRPF8 ENST00000304992.11 protein_altering_variant +PRPF8 ENST00000304992.11 splice_acceptor_variant +PRPF8 ENST00000304992.11 splice_donor_variant +PRPF8 ENST00000304992.11 start_lost +PRPF8 ENST00000304992.11 stop_gained +PRPF8 ENST00000304992.11 stop_lost +PTPN11 ENST00000351677.7 frameshift_variant +PTPN11 ENST00000351677.7 inframe_deletion +PTPN11 ENST00000351677.7 inframe_insertion +PTPN11 ENST00000351677.7 missense_variant +PTPN11 ENST00000351677.7 protein_altering_variant +PTPN11 ENST00000351677.7 splice_acceptor_variant +PTPN11 ENST00000351677.7 splice_donor_variant +PTPN11 ENST00000351677.7 start_lost +PTPN11 ENST00000351677.7 stop_gained +PTPN11 ENST00000351677.7 stop_lost +RUNX1b ENST00000344691.8 frameshift_variant 533-2 724+2 +RUNX1b ENST00000344691.8 inframe_deletion 533-2 724+2 +RUNX1b ENST00000344691.8 inframe_insertion 533-2 724+2 +RUNX1b ENST00000344691.8 missense_variant 533-2 724+2 +RUNX1b ENST00000344691.8 protein_altering_variant 533-2 724+2 +RUNX1b ENST00000344691.8 splice_acceptor_variant 533-2 724+2 +RUNX1b ENST00000344691.8 splice_donor_variant 533-2 724+2 +RUNX1b ENST00000344691.8 start_lost 533-2 724+2 +RUNX1b ENST00000344691.8 stop_gained 533-2 724+2 +RUNX1b ENST00000344691.8 stop_lost 533-2 724+2 +RUNX1 ENST00000675419.1 frameshift_variant +RUNX1 ENST00000675419.1 inframe_deletion +RUNX1 ENST00000675419.1 inframe_insertion +RUNX1 ENST00000675419.1 missense_variant +RUNX1 ENST00000675419.1 protein_altering_variant +RUNX1 ENST00000675419.1 splice_acceptor_variant +RUNX1 ENST00000675419.1 splice_donor_variant +RUNX1 ENST00000675419.1 start_lost +RUNX1 ENST00000675419.1 stop_gained +RUNX1 ENST00000675419.1 stop_lost +SETBP1 ENST00000649279.2 frameshift_variant +SETBP1 ENST00000649279.2 inframe_deletion +SETBP1 ENST00000649279.2 inframe_insertion +SETBP1 ENST00000649279.2 missense_variant +SETBP1 ENST00000649279.2 protein_altering_variant +SETBP1 ENST00000649279.2 splice_acceptor_variant +SETBP1 ENST00000649279.2 splice_donor_variant +SETBP1 ENST00000649279.2 start_lost +SETBP1 ENST00000649279.2 stop_gained +SETBP1 ENST00000649279.2 stop_lost +SF3B1 ENST00000335508.11 frameshift_variant +SF3B1 ENST00000335508.11 inframe_deletion +SF3B1 ENST00000335508.11 inframe_insertion +SF3B1 ENST00000335508.11 missense_variant +SF3B1 ENST00000335508.11 protein_altering_variant +SF3B1 ENST00000335508.11 splice_acceptor_variant +SF3B1 ENST00000335508.11 splice_donor_variant +SF3B1 ENST00000335508.11 start_lost +SF3B1 ENST00000335508.11 stop_gained +SF3B1 ENST00000335508.11 stop_lost +SRSF2 ENST00000359995.10 frameshift_variant +SRSF2 ENST00000359995.10 inframe_deletion +SRSF2 ENST00000359995.10 inframe_insertion +SRSF2 ENST00000359995.10 missense_variant +SRSF2 ENST00000359995.10 protein_altering_variant +SRSF2 ENST00000359995.10 splice_acceptor_variant +SRSF2 ENST00000359995.10 splice_donor_variant +SRSF2 ENST00000359995.10 start_lost +SRSF2 ENST00000359995.10 stop_gained +SRSF2 ENST00000359995.10 stop_lost +STAG2 ENST00000371145.8 frameshift_variant +STAG2 ENST00000371145.8 inframe_deletion +STAG2 ENST00000371145.8 inframe_insertion +STAG2 ENST00000371145.8 missense_variant +STAG2 ENST00000371145.8 protein_altering_variant +STAG2 ENST00000371145.8 splice_acceptor_variant +STAG2 ENST00000371145.8 splice_donor_variant +STAG2 ENST00000371145.8 start_lost +STAG2 ENST00000371145.8 stop_gained +STAG2 ENST00000371145.8 stop_lost +TET2 ENST00000380013.9 frameshift_variant +TET2 ENST00000380013.9 inframe_deletion +TET2 ENST00000380013.9 inframe_insertion +TET2 ENST00000380013.9 missense_variant +TET2 ENST00000380013.9 protein_altering_variant +TET2 ENST00000380013.9 splice_acceptor_variant +TET2 ENST00000380013.9 splice_donor_variant +TET2 ENST00000380013.9 start_lost +TET2 ENST00000380013.9 stop_gained +TET2 ENST00000380013.9 stop_lost +TP53b ENST00000420246.6 frameshift_variant 994-2 *2 +TP53b ENST00000420246.6 inframe_deletion 994-2 *2 +TP53b ENST00000420246.6 inframe_insertion 994-2 *2 +TP53b ENST00000420246.6 missense_variant 994-2 *2 +TP53b ENST00000420246.6 protein_altering_variant 994-2 *2 +TP53b ENST00000420246.6 splice_acceptor_variant 994-2 *2 +TP53b ENST00000420246.6 splice_donor_variant 994-2 *2 +TP53b ENST00000420246.6 start_lost 994-2 *2 +TP53b ENST00000420246.6 stop_gained 994-2 *2 +TP53b ENST00000420246.6 stop_lost 994-2 *2 +TP53 ENST00000269305.9 frameshift_variant +TP53 ENST00000269305.9 inframe_deletion +TP53 ENST00000269305.9 inframe_insertion +TP53 ENST00000269305.9 missense_variant +TP53 ENST00000269305.9 protein_altering_variant +TP53 ENST00000269305.9 splice_acceptor_variant +TP53 ENST00000269305.9 splice_donor_variant +TP53 ENST00000269305.9 start_lost +TP53 ENST00000269305.9 stop_gained +TP53 ENST00000269305.9 stop_lost +TP53g ENST00000455263.6 frameshift_variant 994-2 *2 +TP53g ENST00000455263.6 inframe_deletion 994-2 *2 +TP53g ENST00000455263.6 inframe_insertion 994-2 *2 +TP53g ENST00000455263.6 missense_variant 994-2 *2 +TP53g ENST00000455263.6 protein_altering_variant 994-2 *2 +TP53g ENST00000455263.6 splice_acceptor_variant 994-2 *2 +TP53g ENST00000455263.6 splice_donor_variant 994-2 *2 +TP53g ENST00000455263.6 start_lost 994-2 *2 +TP53g ENST00000455263.6 stop_gained 994-2 *2 +TP53g ENST00000455263.6 stop_lost 994-2 *2 +U2AF1 ENST00000291552.9 frameshift_variant +U2AF1 ENST00000291552.9 inframe_deletion +U2AF1 ENST00000291552.9 inframe_insertion +U2AF1 ENST00000291552.9 missense_variant +U2AF1 ENST00000291552.9 protein_altering_variant +U2AF1 ENST00000291552.9 splice_acceptor_variant +U2AF1 ENST00000291552.9 splice_donor_variant +U2AF1 ENST00000291552.9 start_lost +U2AF1 ENST00000291552.9 stop_gained +U2AF1 ENST00000291552.9 stop_lost +UBA1 ENST00000335972.11 frameshift_variant +UBA1 ENST00000335972.11 inframe_deletion +UBA1 ENST00000335972.11 inframe_insertion +UBA1 ENST00000335972.11 missense_variant +UBA1 ENST00000335972.11 protein_altering_variant +UBA1 ENST00000335972.11 splice_acceptor_variant +UBA1 ENST00000335972.11 splice_donor_variant +UBA1 ENST00000335972.11 start_lost +UBA1 ENST00000335972.11 stop_gained +UBA1 ENST00000335972.11 stop_lost +WT1 ENST00000452863.10 frameshift_variant +WT1 ENST00000452863.10 inframe_deletion +WT1 ENST00000452863.10 inframe_insertion +WT1 ENST00000452863.10 missense_variant +WT1 ENST00000452863.10 protein_altering_variant +WT1 ENST00000452863.10 splice_acceptor_variant +WT1 ENST00000452863.10 splice_donor_variant +WT1 ENST00000452863.10 start_lost +WT1 ENST00000452863.10 stop_gained +WT1 ENST00000452863.10 stop_lost +ZRSR2 ENST00000307771.8 frameshift_variant +ZRSR2 ENST00000307771.8 inframe_deletion +ZRSR2 ENST00000307771.8 inframe_insertion +ZRSR2 ENST00000307771.8 missense_variant +ZRSR2 ENST00000307771.8 protein_altering_variant +ZRSR2 ENST00000307771.8 splice_acceptor_variant +ZRSR2 ENST00000307771.8 splice_donor_variant +ZRSR2 ENST00000307771.8 start_lost +ZRSR2 ENST00000307771.8 stop_gained +ZRSR2 ENST00000307771.8 stop_lost