Increase SETH's coverage of mutations contained HGVS
rockt opened this issue · 1 comments
Add test cases for the following mentions and then change the grammar to account for them:
2 c.2235_2252>AAT
2 p.G536>?
2 p.(I1290)fs
2 p.A67_M72>V
2 p.(L1515)fs
2 c.7521_7540>TCTCCTACC
2 p.L243>GCI
2 p.N567_L576>I
2 p.(K1322)fs
2 p.L242>CWMK
2 p.S566_E571>K
2 p.E57_D58>DY
2 p.L747_K754>N
2 c.522+-155delTCAGATTGTGGTGGAGGAAG
2 p.S704>?
2 c.528_529ins?
2 p.D148_G149>ES
2 p.F537_I540>LV
2 p.Q439_T440>PP
2 p.M979_K980>I*
2 p.G607>?
2 p.L243>RCPS
2 p.A19>?
2 p.E749_E758>QP
2 p.L242_T244>FTCPS
2 p.R583>?
2 p.L242>FSCGP
2 p.H594_P595>PT
2 c.2239_2264>GCCAA
2 p.G1050>?
2 p.L747_E749>C
2 p.M552_V559>I
2 c.481_482ins?
2 p.E746_A750>EP
2 p.S1278_F1279>F
2 p.L308_S312>P
2 p.556_871dup
2 p.E709_T710>D
2 p.L242>FDCIGV
2 p.R216>?
2 p.E185_E186>D*
2 p.E709_T710>A
2 p.Q1168>HE
2 p.I843_S847>L
2 p.N567_Y578>ED
2 c.2236_2248>CAAC
2 c.713+8insAGT
2 p.I245_S246>SHQPC
2 p.Q556_K558>PT
2 p.N443>?
2 p.H776_C777>QS
2 p.D627_L633>E
2 p.L243>CPSP
2 p.Q612_R613>HC
2 p.I245_S246>HRGC
2 p.S374_E375>R*
2 p.T751_E758>A
2 p.G346>?
2 p.P272>?
2 p.G1283>?
2 p.P761>?
2 p.A166>?
2 p.K579_H580>ND
2 p.L125_H126>FY
2 p.I1676_V1677>I
2 p.G248>?
2 p.N406_L407>M
2 p.P10>QS
2 p.V8226>?
2 p.L380>?
2 p.L146_G147>FC
2 c.1072_1073CC>11
2 p.T751_I759>N
2 p.264_265insSSGNL
2 p.V192>?
2 p.(550_592)ins7
2 p.S1530>?
2 p.I8521>SL
2 p.L242_T243>CGIREI
2 p.K94_T95>NP
2 p.L243_T244>PIYRCVL
2 p.W557_V559>F
2 p.A89>?
2 p.P325>?
2 p.L747_P753>Q
2 p.E224_I227>V
2 c.405_406ins?
2 p.L112_E113>*
2 p.T244>KKCTN
2 p.R152_I153>SF
2 c.252_253ins?
2 p.V600>DLAT
2 p.P52>?
2 c.461_462ins?
2 p.W15475>?
2 p.
2 p.I241_L242>CRPH
2 c.236+-6delAGCGAAGGT
2 p.L242_T244>CPP
2 c.2230_2249>GTCAA
2 p.T392>?
2 c.2235_2251>AATTC
2 p.G464>?
2 p.W334_P335>CS
2 p.(Q1434)fs
2 p.C5_D7>Y
2 c.2235_2248>AATTC
2 c.457_458ins?
2 p.K459_S460>N
2 c.4191+-4delCTGAGGTATTAATTATATATA
2 p.E1138>?
2 p.K664_K665>N*
2 p.I2752>?
2 p.D523_P524>EA
2 c.4455+-25delGCCAGCAAGGTGAACCGGGTCCAAAGG
2 p.S1280>?
2 p.?fs_?
2 p.Y553_L576>NCLHLYSSQ
2 p.P1139>?
2 p.G15_L16>GF
2 p.K896_F897>I
2 p.L747_K754>GC
2 c.3999+2insT
2 p.L243_T244>PLCSA
2 c.184_185ins?
2 p.Q341_G347>H
2 p.E237_L242>ASWC
2 p.E746_A750>IP
2 c.743_755>GTCAAAG
2 p.P775>?
2 p.G244_M246>V
2 c.182_183ins?
2 p.E746_T751>IP
2 c.2235_2251>AG
2 p.F375_P376>S
2 p.E746_A750>QP
2 p.L1386_Q1387>L_
2 p.W5642>?
2 c.281_282ins?
2 p.fs_?
2 p.Q119_A123>H
2 p.E289_A290>DT
2 p.S80_P81>T
2 p.Q556_V559>H
2 p.(N216)fs
2 p.L747_T751>Q
2 p.L747_T751>S
2 p.E180>DGRCPHQ
2 p.N1375_A1376>KS
2 p.T98>?
2 c.710_726>CCTCCTGGTGC
2 p.L948>?
2 p.E434_H435>D
2 p.L248_S251>CQ
2 p.D770_P772>ASVDNR
2 p.L64_E69>Q
2 p.N995_G996>K
2 p.I247>KCH
2 p.I744_A750>VK
2 p.D210_L211>EI
2 c.2235_2255>GGT
2 p.F1607_K1608>LGSQ
2 p.fs?
2 p.L242>FEC
2 p.K558_T574>NRS
2 p.G284_P287>A
2 p.L747_P753>CG
2 p.A254_L255>EKV
2 p.P551_Q556>T
2 p.L306_G307>FW
2 p.L243_T244>PCPL
2 p.E519>D_
2 c.105_144>TTC
2 p.S215_V218>R
2 p.E1053_Y1054>DH
2 c.157_158ins?
2 p.T325_C328>S
4 p.S566_E571>R
4 c.2239_2251>C
4 p.E746_T751>I
4 p.N771_P772>SVDNR
4 p.V600_K601>E
6 p.E746_T751>A
6 p.L747_A750>P
6 p.L747_T751>P
6 c.2237_2255>T
6 c.?ins?
18 p.E746_S752>V
18 p.0
20 p.L747_P753>S
26 p.??ins?
32 c.??ins?
32 p.?del
34 p.0?
44 p.?fs
558 c.?
1812 p.?
changed grammar to account for the following mentions:
c.2235_2251>AG (exact grammar)
p.K896_F897>I (non exact grammar)
p.(K1322)fs (exact grammar)
p.(Cys28_Lys29delinsTrp) (non exact grammar)
p.0 (exact grammar)
p.0? (exact grammar)
c.252_253ins? (exact grammar)
the grammar was NOT adapted to account for the following mentions, which are not consistent with any nomenclature:
p.556_871dup (missing amino acids)
p. (too unspecific)
p.? (too unspecific)
p.?fs (too unspecific)
p.?del (too unspecific)
p.fs_? (too unspecific)
p.fs? (too unspecific)
p.?fs_? (too unspecific)
p.??ins? (too unspecific)
c.?ins? (too unspecific)
c.??ins? (too unspecific)
c.? (too unspecific)
c.236+-6delAGCGAAGGT (+ and - at the same time)
c.713+8insAGT (correct grammar would be: c.713+8_713+9insAGT)