Disease associated variation - ClinVar Allele ID Type Name RS#dbSNP Phenotype IDs Chromosome Start Stop Reference Alternate 39255 deletion NM_004656.3(BAP1):c.1305delG (p.Gln436Asnfs) 587776877 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52437856 52437856 C - 39255 deletion NM_004656.3(BAP1):c.1305delG (p.Gln436Asnfs) 587776877 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52403840 52403840 C - 39256 single nucleotide variant NM_004656.3(BAP1):c.2057-2A>G 587776878 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52436439 52436439 T C 39256 single nucleotide variant NM_004656.3(BAP1):c.2057-2A>G 587776878 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52402423 52402423 T C 39257 single nucleotide variant NM_004656.3(BAP1):c.438-2A>G 587776879 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52441334 52441334 T C 39257 single nucleotide variant NM_004656.3(BAP1):c.438-2A>G 587776879 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52407318 52407318 T C 39258 single nucleotide variant NM_004656.3(BAP1):c.2050C>T (p.Gln684Ter) 387906848 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52436624 52436624 G A 39258 single nucleotide variant NM_004656.3(BAP1):c.2050C>T (p.Gln684Ter) 387906848 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52402608 52402608 G A 39259 deletion BAP1, 1-BP DEL, 1832C -1 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 na -1 -1 na na 39260 deletion BAP1, 4-BP DEL, 2008TCAC -1 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 na -1 -1 na na 39261 single nucleotide variant NM_004656.3(BAP1):c.799C>T (p.Gln267Ter) 387906849 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52439913 52439913 G A 39261 single nucleotide variant NM_004656.3(BAP1):c.799C>T (p.Gln267Ter) 387906849 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52405897 52405897 G A 70526 deletion NM_004656.3(BAP1):c.78_79delGG (p.Val27Alafs) 397509413 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52443613 52443614 CC - 70526 deletion NM_004656.3(BAP1):c.78_79delGG (p.Val27Alafs) 397509413 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52409597 52409598 CC - 70527 single nucleotide variant NM_004656.3(BAP1):c.277A>G (p.Thr93Ala) 375129361 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52442072 52442072 T C 70527 single nucleotide variant NM_004656.3(BAP1):c.277A>G (p.Thr93Ala) 375129361 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52408056 52408056 T C 70528 deletion NM_004656.3(BAP1):c.1654delG (p.Asp552Ilefs) 397509414 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52437507 52437507 C - 70528 deletion NM_004656.3(BAP1):c.1654delG (p.Asp552Ilefs) 397509414 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52403491 52403491 C - 137400 single nucleotide variant NM_004656.3(BAP1):c.905C>T (p.Pro302Leu) 149158790 MedGen:CN169374 3 52439807 52439807 G A 137400 single nucleotide variant NM_004656.3(BAP1):c.905C>T (p.Pro302Leu) 149158790 MedGen:CN169374 3 52405791 52405791 G A 137401 single nucleotide variant NM_004656.3(BAP1):c.1325C>G (p.Pro442Arg) 587778089 MedGen:CN169374 3 52437836 52437836 G C 137401 single nucleotide variant NM_004656.3(BAP1):c.1325C>G (p.Pro442Arg) 587778089 MedGen:CN169374 3 52403820 52403820 G C 137402 single nucleotide variant NM_004656.3(BAP1):c.1408G>A (p.Gly470Arg) 576538858 MedGen:CN169374 3 52437753 52437753 C T 137402 single nucleotide variant NM_004656.3(BAP1):c.1408G>A (p.Gly470Arg) 576538858 MedGen:CN169374 3 52403737 52403737 C T 137403 single nucleotide variant NM_004656.3(BAP1):c.1786A>G (p.Ser596Gly) 79014342 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539;MedGen:CN169374 3 52437258 52437258 T C 137403 single nucleotide variant NM_004656.3(BAP1):c.1786A>G (p.Ser596Gly) 79014342 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539;MedGen:CN169374 3 52403242 52403242 T C 137404 single nucleotide variant NM_004656.3(BAP1):c.1838C>T (p.Thr613Met) 35448940 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539;MedGen:CN169374 3 52437206 52437206 G A 137404 single nucleotide variant NM_004656.3(BAP1):c.1838C>T (p.Thr613Met) 35448940 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539;MedGen:CN169374 3 52403190 52403190 G A 137405 single nucleotide variant NM_004656.3(BAP1):c.1735G>A (p.Gly579Arg) 370004702 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539;MedGen:CN169374 3 52437309 52437309 C T 137405 single nucleotide variant NM_004656.3(BAP1):c.1735G>A (p.Gly579Arg) 370004702 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539;MedGen:CN169374 3 52403293 52403293 C T 137406 single nucleotide variant NM_004656.3(BAP1):c.121G>A (p.Gly41Ser) 372586694 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539;MedGen:CN169374 3 52443571 52443571 C T 137406 single nucleotide variant NM_004656.3(BAP1):c.121G>A (p.Gly41Ser) 372586694 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539;MedGen:CN169374 3 52409555 52409555 C T 221420 single nucleotide variant NM_004656.3(BAP1):c.1026C>T (p.Ser342=) 71651686 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539;MedGen:CN169374 3 52439216 52439216 G A 221420 single nucleotide variant NM_004656.3(BAP1):c.1026C>T (p.Ser342=) 71651686 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539;MedGen:CN169374 3 52405200 52405200 G A 221421 single nucleotide variant NM_004656.3(BAP1):c.1002A>G (p.Leu334=) 28997577 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539;MedGen:CN169374 3 52439240 52439240 T C 221421 single nucleotide variant NM_004656.3(BAP1):c.1002A>G (p.Leu334=) 28997577 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539;MedGen:CN169374 3 52405224 52405224 T C 221422 single nucleotide variant NM_004656.3(BAP1):c.778C>T (p.Gln260Ter) 864622592 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52406258 52406258 G A 221422 single nucleotide variant NM_004656.3(BAP1):c.778C>T (p.Gln260Ter) 864622592 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52440274 52440274 G A 222989 deletion NM_004656.3(BAP1):c.1717delC (p.Leu573Trpfs) 869025212 MedGen:CN235077 3 52437444 52437444 G - 222989 deletion NM_004656.3(BAP1):c.1717delC (p.Leu573Trpfs) 869025212 MedGen:CN235077 3 52403428 52403428 G - 225228 single nucleotide variant NM_004656.3(BAP1):c.1116+81T>C 869312491 MedGen:C0027672,SNOMED CT:C0027672 3 52439045 52439045 A G 225228 single nucleotide variant NM_004656.3(BAP1):c.1116+81T>C 869312491 MedGen:C0027672,SNOMED CT:C0027672 3 52405029 52405029 A G 225229 single nucleotide variant NM_004656.3(BAP1):c.1116+254T>G 545879955 MedGen:C0027672,SNOMED CT:C0027672 3 52404856 52404856 A C 225229 single nucleotide variant NM_004656.3(BAP1):c.1116+254T>G 545879955 MedGen:C0027672,SNOMED CT:C0027672 3 52438872 52438872 A C 225230 single nucleotide variant NM_004656.3(BAP1):c.932-51T>A 869312492 MedGen:C0027672,SNOMED CT:C0027672 3 52405345 52405345 A T 225230 single nucleotide variant NM_004656.3(BAP1):c.932-51T>A 869312492 MedGen:C0027672,SNOMED CT:C0027672 3 52439361 52439361 A T 225231 single nucleotide variant NM_004656.3(BAP1):c.1116+83G>A 576117601 MedGen:C0027672,SNOMED CT:C0027672 3 52439043 52439043 C T 225231 single nucleotide variant NM_004656.3(BAP1):c.1116+83G>A 576117601 MedGen:C0027672,SNOMED CT:C0027672 3 52405027 52405027 C T 225232 single nucleotide variant NM_004656.3(BAP1):c.660-26T>A 139414598 MedGen:C0027672,SNOMED CT:C0027672 3 52440418 52440418 A T 225232 single nucleotide variant NM_004656.3(BAP1):c.660-26T>A 139414598 MedGen:C0027672,SNOMED CT:C0027672 3 52406402 52406402 A T 225233 single nucleotide variant NM_004656.3(BAP1):c.375+30C>T 756955810 MedGen:C0027672,SNOMED CT:C0027672 3 52407928 52407928 G A 225233 single nucleotide variant NM_004656.3(BAP1):c.375+30C>T 756955810 MedGen:C0027672,SNOMED CT:C0027672 3 52441944 52441944 G A 225234 single nucleotide variant NM_004656.3(BAP1):c.1891-122G>A 869312493 MedGen:C0027672,SNOMED CT:C0027672 3 52402993 52402993 C T 225234 single nucleotide variant NM_004656.3(BAP1):c.1891-122G>A 869312493 MedGen:C0027672,SNOMED CT:C0027672 3 52437009 52437009 C T 225235 single nucleotide variant NM_004656.3(BAP1):c.2057-22A>C 144083199 MedGen:C0027672,SNOMED CT:C0027672 3 52402443 52402443 T G 225235 single nucleotide variant NM_004656.3(BAP1):c.2057-22A>C 144083199 MedGen:C0027672,SNOMED CT:C0027672 3 52436459 52436459 T G 225236 single nucleotide variant NM_004656.3(BAP1):c.932-38C>T 200846682 MedGen:C0027672,SNOMED CT:C0027672 3 52439348 52439348 G A 225236 single nucleotide variant NM_004656.3(BAP1):c.932-38C>T 200846682 MedGen:C0027672,SNOMED CT:C0027672 3 52405332 52405332 G A 225237 single nucleotide variant NM_004656.3(BAP1):c.122+291C>T 569715214 MedGen:C0027672,SNOMED CT:C0027672 3 52409263 52409263 G A 225237 single nucleotide variant NM_004656.3(BAP1):c.122+291C>T 569715214 MedGen:C0027672,SNOMED CT:C0027672 3 52443279 52443279 G A 226316 single nucleotide variant NM_004656.3(BAP1):c.1063C>T (p.Gln355Ter) 869312757 MedGen:C0027672,SNOMED CT:C0027672 3 52405163 52405163 G A 226316 single nucleotide variant NM_004656.3(BAP1):c.1063C>T (p.Gln355Ter) 869312757 MedGen:C0027672,SNOMED CT:C0027672 3 52439179 52439179 G A 231631 deletion NM_004656.3(BAP1):c.783+4_783+13delGGTGCCCTTT 876661262 MedGen:CN169374 3 52406240 52406249 AAAGGGCACC - 231631 deletion NM_004656.3(BAP1):c.783+4_783+13delGGTGCCCTTT 876661262 MedGen:CN169374 3 52440256 52440265 AAAGGGCACC - 239258 single nucleotide variant NM_004656.3(BAP1):c.2091C>T (p.Ser697=) 754513396 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52402387 52402387 G A 239258 single nucleotide variant NM_004656.3(BAP1):c.2091C>T (p.Ser697=) 754513396 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52436403 52436403 G A 239259 single nucleotide variant NM_004656.3(BAP1):c.2057-4G>T 149499021 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539;MedGen:CN169374 3 52436441 52436441 C A 239259 single nucleotide variant NM_004656.3(BAP1):c.2057-4G>T 149499021 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539;MedGen:CN169374 3 52402425 52402425 C A 239260 single nucleotide variant NM_004656.3(BAP1):c.1962A>C (p.Val654=) 148624125 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52436816 52436816 T G 239260 single nucleotide variant NM_004656.3(BAP1):c.1962A>C (p.Val654=) 148624125 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52402800 52402800 T G 239261 single nucleotide variant NM_004656.3(BAP1):c.1946G>A (p.Cys649Tyr) 151308667 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52436832 52436832 C T 239261 single nucleotide variant NM_004656.3(BAP1):c.1946G>A (p.Cys649Tyr) 151308667 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52402816 52402816 C T 239262 single nucleotide variant NM_004656.3(BAP1):c.1749G>A (p.Ser583=) 147775249 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52437295 52437295 C T 239262 single nucleotide variant NM_004656.3(BAP1):c.1749G>A (p.Ser583=) 147775249 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52403279 52403279 C T 239263 single nucleotide variant NM_004656.3(BAP1):c.1729+8T>C 150945583 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539;MedGen:CN169374 3 52437424 52437424 A G 239263 single nucleotide variant NM_004656.3(BAP1):c.1729+8T>C 150945583 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539;MedGen:CN169374 3 52403408 52403408 A G 239264 single nucleotide variant NM_004656.3(BAP1):c.1548G>A (p.Pro516=) 148990823 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52403597 52403597 C T 239264 single nucleotide variant NM_004656.3(BAP1):c.1548G>A (p.Pro516=) 148990823 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52437613 52437613 C T 239265 single nucleotide variant NM_004656.3(BAP1):c.1427T>C (p.Val476Ala) 144060813 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52437734 52437734 A G 239265 single nucleotide variant NM_004656.3(BAP1):c.1427T>C (p.Val476Ala) 144060813 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52403718 52403718 A G 239266 single nucleotide variant NM_004656.3(BAP1):c.1407C>T (p.Ser469=) 150524807 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52437754 52437754 G A 239266 single nucleotide variant NM_004656.3(BAP1):c.1407C>T (p.Ser469=) 150524807 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52403738 52403738 G A 239267 single nucleotide variant NM_004656.3(BAP1):c.1344G>A (p.Leu448=) 368684241 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52437817 52437817 C T 239267 single nucleotide variant NM_004656.3(BAP1):c.1344G>A (p.Leu448=) 368684241 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52403801 52403801 C T 239268 single nucleotide variant NM_004656.3(BAP1):c.1268C>A (p.Thr423Lys) 115109161 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52437893 52437893 G T 239268 single nucleotide variant NM_004656.3(BAP1):c.1268C>A (p.Thr423Lys) 115109161 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52403877 52403877 G T 239269 single nucleotide variant NM_004656.3(BAP1):c.1250+7C>G 878854738 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52404446 52404446 G C 239269 single nucleotide variant NM_004656.3(BAP1):c.1250+7C>G 878854738 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52438462 52438462 G C 239270 single nucleotide variant NM_004656.3(BAP1):c.1217A>T (p.Glu406Val) 535695655 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52438502 52438502 T A 239270 single nucleotide variant NM_004656.3(BAP1):c.1217A>T (p.Glu406Val) 535695655 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52404486 52404486 T A 239271 single nucleotide variant NM_004656.3(BAP1):c.1147C>T (p.Arg383Cys) 201844078 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52438572 52438572 G A 239271 single nucleotide variant NM_004656.3(BAP1):c.1147C>T (p.Arg383Cys) 201844078 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52404556 52404556 G A 239272 single nucleotide variant NM_004656.3(BAP1):c.1035G>C (p.Gly345=) 369744075 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52439207 52439207 C G 239272 single nucleotide variant NM_004656.3(BAP1):c.1035G>C (p.Gly345=) 369744075 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52405191 52405191 C G 239273 single nucleotide variant NM_004656.3(BAP1):c.960C>T (p.Cys320=) 143659795 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52439282 52439282 G A 239273 single nucleotide variant NM_004656.3(BAP1):c.960C>T (p.Cys320=) 143659795 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52405266 52405266 G A 239274 single nucleotide variant NM_004656.3(BAP1):c.932-8T>C 878854743 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52439318 52439318 A G 239274 single nucleotide variant NM_004656.3(BAP1):c.932-8T>C 878854743 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52405302 52405302 A G 239275 single nucleotide variant NM_004656.3(BAP1):c.878C>T (p.Pro293Leu) 777664260 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52439834 52439834 G A 239275 single nucleotide variant NM_004656.3(BAP1):c.878C>T (p.Pro293Leu) 777664260 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52405818 52405818 G A 239276 single nucleotide variant NM_004656.3(BAP1):c.783G>A (p.Gln261=) 35003777 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539;MedGen:CN169374 3 52440269 52440269 C T 239276 single nucleotide variant NM_004656.3(BAP1):c.783G>A (p.Gln261=) 35003777 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539;MedGen:CN169374 3 52406253 52406253 C T 239277 single nucleotide variant NM_004656.3(BAP1):c.779A>G (p.Gln260Arg) 878854742 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52440273 52440273 T C 239277 single nucleotide variant NM_004656.3(BAP1):c.779A>G (p.Gln260Arg) 878854742 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52406257 52406257 T C 239278 single nucleotide variant NM_004656.3(BAP1):c.659+3A>C 878854741 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52440842 52440842 T G 239278 single nucleotide variant NM_004656.3(BAP1):c.659+3A>C 878854741 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52406826 52406826 T G 239279 single nucleotide variant NM_004656.3(BAP1):c.626T>C (p.Val209Ala) 878854740 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52440878 52440878 A G 239279 single nucleotide variant NM_004656.3(BAP1):c.626T>C (p.Val209Ala) 878854740 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52406862 52406862 A G 239280 single nucleotide variant NM_004656.3(BAP1):c.581-9C>G 878854739 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52440932 52440932 G C 239280 single nucleotide variant NM_004656.3(BAP1):c.581-9C>G 878854739 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52406916 52406916 G C 239281 single nucleotide variant NM_004656.3(BAP1):c.534C>T (p.Gly178=) 200285587 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52441236 52441236 G A 239281 single nucleotide variant NM_004656.3(BAP1):c.534C>T (p.Gly178=) 200285587 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52407220 52407220 G A 239282 single nucleotide variant NM_004656.3(BAP1):c.519T>C (p.Tyr173=) 143901408 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52441251 52441251 A G 239282 single nucleotide variant NM_004656.3(BAP1):c.519T>C (p.Tyr173=) 143901408 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52407235 52407235 A G 239283 single nucleotide variant NM_004656.3(BAP1):c.501G>A (p.Ala167=) 148631953 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52441269 52441269 C T 239283 single nucleotide variant NM_004656.3(BAP1):c.501G>A (p.Ala167=) 148631953 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52407253 52407253 C T 239284 single nucleotide variant NM_004656.3(BAP1):c.448C>T (p.Arg150Cys) 548946316 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52441322 52441322 G A 239284 single nucleotide variant NM_004656.3(BAP1):c.448C>T (p.Arg150Cys) 548946316 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52407306 52407306 G A 239285 single nucleotide variant NM_004656.3(BAP1):c.376-4G>A 369277958 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52441480 52441480 C T 239285 single nucleotide variant NM_004656.3(BAP1):c.376-4G>A 369277958 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52407464 52407464 C T 239286 single nucleotide variant NM_004656.3(BAP1):c.288G>A (p.Leu96=) 117382883 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52408045 52408045 C T 239286 single nucleotide variant NM_004656.3(BAP1):c.288G>A (p.Leu96=) 117382883 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52442061 52442061 C T 239287 single nucleotide variant NM_004656.3(BAP1):c.177G>A (p.Arg59=) 770446947 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52442568 52442568 C T 239287 single nucleotide variant NM_004656.3(BAP1):c.177G>A (p.Arg59=) 770446947 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52408552 52408552 C T 251242 single nucleotide variant NM_004656.3(BAP1):c.294C>T (p.Ser98=) 140641333 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539;MedGen:CN169374 3 52408039 52408039 G A 251242 single nucleotide variant NM_004656.3(BAP1):c.294C>T (p.Ser98=) 140641333 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539;MedGen:CN169374 3 52442055 52442055 G A 274513 single nucleotide variant NM_004656.3(BAP1):c.961G>A (p.Ala321Thr) 143891879 MedGen:CN169374 3 52439281 52439281 C T 274513 single nucleotide variant NM_004656.3(BAP1):c.961G>A (p.Ala321Thr) 143891879 MedGen:CN169374 3 52405265 52405265 C T 291178 single nucleotide variant NM_004656.3(BAP1):c.*697G>A 766301450 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52401591 52401591 C T 291178 single nucleotide variant NM_004656.3(BAP1):c.*697G>A 766301450 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52435607 52435607 C T 291179 single nucleotide variant NM_004656.3(BAP1):c.*60C>T 564062251 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52402228 52402228 G A 291179 single nucleotide variant NM_004656.3(BAP1):c.*60C>T 564062251 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52436244 52436244 G A 291182 single nucleotide variant NM_004656.3(BAP1):c.*45C>G 56898787 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52402243 52402243 G C 291182 single nucleotide variant NM_004656.3(BAP1):c.*45C>G 56898787 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52436259 52436259 G C 291187 single nucleotide variant NM_004656.3(BAP1):c.341G>A (p.Arg114His) 773494626 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52407992 52407992 C T 291187 single nucleotide variant NM_004656.3(BAP1):c.341G>A (p.Arg114His) 773494626 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52442008 52442008 C T 292129 single nucleotide variant NM_004656.3(BAP1):c.*1164G>C 376927338 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52401124 52401124 C G 292129 single nucleotide variant NM_004656.3(BAP1):c.*1164G>C 376927338 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52435140 52435140 C G 292131 single nucleotide variant NM_004656.3(BAP1):c.*1064C>T 886058700 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52401224 52401224 G A 292131 single nucleotide variant NM_004656.3(BAP1):c.*1064C>T 886058700 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52435240 52435240 G A 292134 single nucleotide variant NM_004656.3(BAP1):c.*552C>A 886058702 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52401736 52401736 G T 292134 single nucleotide variant NM_004656.3(BAP1):c.*552C>A 886058702 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52435752 52435752 G T 292135 single nucleotide variant NM_004656.3(BAP1):c.*444C>T 123598 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52401844 52401844 G A 292135 single nucleotide variant NM_004656.3(BAP1):c.*444C>T 123598 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52435860 52435860 G A 292136 single nucleotide variant NM_004656.3(BAP1):c.1338C>T (p.Asn446=) 763735807 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52403807 52403807 G A 292136 single nucleotide variant NM_004656.3(BAP1):c.1338C>T (p.Asn446=) 763735807 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52437823 52437823 G A 292137 deletion NM_004656.3(BAP1):c.1202_1203delAT (p.Tyr401Terfs) 886058705 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52404500 52404501 AT - 292137 deletion NM_004656.3(BAP1):c.1202_1203delAT (p.Tyr401Terfs) 886058705 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52438516 52438517 AT - 292138 single nucleotide variant NM_004656.3(BAP1):c.931+10G>C 199560386 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52405755 52405755 C G 292138 single nucleotide variant NM_004656.3(BAP1):c.931+10G>C 199560386 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52439771 52439771 C G 292145 single nucleotide variant NM_004656.3(BAP1):c.581-6C>T 754576458 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52406913 52406913 G A 292145 single nucleotide variant NM_004656.3(BAP1):c.581-6C>T 754576458 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52440929 52440929 G A 292146 single nucleotide variant NM_004656.3(BAP1):c.74A>G (p.Lys25Arg) 759337168 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52409602 52409602 T C 292146 single nucleotide variant NM_004656.3(BAP1):c.74A>G (p.Lys25Arg) 759337168 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52443618 52443618 T C 295531 single nucleotide variant NM_004656.3(BAP1):c.*830T>C 886058701 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52401458 52401458 A G 295531 single nucleotide variant NM_004656.3(BAP1):c.*830T>C 886058701 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52435474 52435474 A G 295532 single nucleotide variant NM_004656.3(BAP1):c.*643G>A 374367093 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52401645 52401645 C T 295532 single nucleotide variant NM_004656.3(BAP1):c.*643G>A 374367093 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52435661 52435661 C T 295536 single nucleotide variant NM_004656.3(BAP1):c.*485G>T 886058703 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52401803 52401803 C A 295536 single nucleotide variant NM_004656.3(BAP1):c.*485G>T 886058703 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52435819 52435819 C A 295537 single nucleotide variant NM_004656.3(BAP1):c.1497C>T (p.Ile499=) 777417522 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52403648 52403648 G A 295537 single nucleotide variant NM_004656.3(BAP1):c.1497C>T (p.Ile499=) 777417522 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52437664 52437664 G A 295561 single nucleotide variant NM_004656.3(BAP1):c.1413T>G (p.Ala471=) 34736117 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52403732 52403732 A C 295561 single nucleotide variant NM_004656.3(BAP1):c.1413T>G (p.Ala471=) 34736117 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52437748 52437748 A C 295571 single nucleotide variant NM_004656.3(BAP1):c.-10C>T 200018055 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52409888 52409888 G A 295571 single nucleotide variant NM_004656.3(BAP1):c.-10C>T 200018055 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52443904 52443904 G A 295685 single nucleotide variant NM_004656.3(BAP1):c.*974C>T 9855479 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52401314 52401314 G A 295685 single nucleotide variant NM_004656.3(BAP1):c.*974C>T 9855479 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52435330 52435330 G A 295687 single nucleotide variant NM_004656.3(BAP1):c.*222G>C 886058704 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52402066 52402066 C G 295687 single nucleotide variant NM_004656.3(BAP1):c.*222G>C 886058704 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52436082 52436082 C G 295688 single nucleotide variant NM_004656.3(BAP1):c.*37G>A 139307137 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52402251 52402251 C T 295688 single nucleotide variant NM_004656.3(BAP1):c.*37G>A 139307137 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52436267 52436267 C T 295699 single nucleotide variant NM_004656.3(BAP1):c.1791C>T (p.Ser597=) 751730111 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52403237 52403237 G A 295699 single nucleotide variant NM_004656.3(BAP1):c.1791C>T (p.Ser597=) 751730111 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52437253 52437253 G A 295700 single nucleotide variant NM_004656.3(BAP1):c.908C>T (p.Ala303Val) 753460994 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52405788 52405788 G A 295700 single nucleotide variant NM_004656.3(BAP1):c.908C>T (p.Ala303Val) 753460994 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52439804 52439804 G A 295707 single nucleotide variant NM_004656.3(BAP1):c.821A>C (p.His274Pro) 565400314 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52405875 52405875 T G 295707 single nucleotide variant NM_004656.3(BAP1):c.821A>C (p.His274Pro) 565400314 MedGen:C3280492,OMIM:614327,Orphanet:ORPHA289539 3 52439891 52439891 T G

Disease associated variation - GWASdb Chr Pos SNP ID(dbSNP 142) Ref Alt Ori SNP ID P-value Drug Name Drug Anno GWAS Trait HPO ID DO ID AA Type Trait or Drug 1 185071735 rs34982714 A AC rs34982714 3.50E-08 Urinary metabolites HPOID:0000079 DOID:557 A UTR-3 GWASdb_trait

Disease associated variation - GWAS Central Study Name Source Marker Accession Chromosome Marker Start Marker Stop Alleles Gene Section P-value -log(p-value) GWAS of prostate cancer rs6684195 1 185026813 185026813 intronic 0.901678 0.044948526526765106 GWAS of prostate cancer rs12038919 1 185041630 185041630 intronic 0.641546 0.19277219847855 GWAS of prostate cancer rs7519019 1 185038104 185038104 intronic 0.405163 0.392370221824897 GWAS of prostate cancer rs12127009 1 185030547 185030547 intronic 0.285488 0.544412141860551

Disease associated variation - OMIM Ensembl_gene_ID Approved Gene Symbol MIM Number ENSG00000121481.10 RNF2 608985