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Merged
Redmar-van-den-Berg merged 10 commits into from
Feb 10, 2026
Merged

fixes in criteria for inclusion and annotation #49

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fcb7baa
include gene MPL and delete duplicate rows
AnnevdGrinten Feb 2, 2026
27375ea
fix nr of columns for MPL
AnnevdGrinten Feb 2, 2026
d6ed06d
Add start end for alt exon transcripts TP53 RUNX1
AnnevdGrinten Feb 2, 2026
eea1825
Add protein_altering_variant
AnnevdGrinten Feb 2, 2026
b4b3d54
change `discard` to `likely benign`
AnnevdGrinten Feb 2, 2026
6330ca4
change `discard` to `likely benign`
AnnevdGrinten Feb 3, 2026
48b65b1
unify logic for all genes
AnnevdGrinten Feb 3, 2026
a9c2e7d
add gene MPL
AnnevdGrinten Feb 3, 2026
84a7f2c
Annotate other variants in WT1 ex7+9 `possible pathogenic`
AnnevdGrinten Feb 10, 2026
a73ce99
Add more known pathogenic variants
AnnevdGrinten Feb 10, 2026
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4 changes: 2 additions & 2 deletions docs/source/snv-indels.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down
185 changes: 117 additions & 68 deletions utilities/deps/small-files/annotation_criteria.tsv
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Original file line number Diff line number Diff line change
@@ -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
Expand All @@ -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
RAD21 ENST00000297338.7 possible pathogenic
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