ClinVar Miner

Variants in gene SMPD1 with conflicting interpretations

See also:
Y axis minimum submission review status: Y axis collection method:
X axis minimum submission review status: X axis collection method:
Minimum conflict level:
Gene type:

If a variant has more than two submissions, it may have multiple conflicts and therefore be counted in more than one conflict column. If this is the case, the "Variants with any kind of conflict" cell will be less than the sum of the conflicted variants cells to its left.

Variants with only 1 submission per condition Variants with at least 2 submissions on the same condition and no conflicts Variants with a synonymous conflict
(e.g. benign vs non-pathogenic)
Variants with a confidence conflict
(e.g. benign vs likely benign)
Variants with a benign or likely benign vs uncertain conflict Variants with a category conflict
(e.g. benign vs affects)
Variants with a clinically significant conflict
(e.g. benign vs pathogenic)
Variants with any conflict
925 94 0 84 35 0 26 133

Significance breakdown #

In the table below, cells that correspond to a term paired with itself represent synonymous conflicts, i.e. variants that have been annotated with different terms that map to the same standard term. To compare the terms that were actually submitted, check the box in the filters section at the top of this page.

pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 68 7 1 0
likely pathogenic 68 0 24 0 0
uncertain significance 7 24 0 33 4
likely benign 1 0 33 0 16
benign 0 0 4 16 0

All variants with conflicting interpretations #

Total variants: 133
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000543.5(SMPD1):c.1487-36C>T rs11601088 0.10497
NM_000543.5(SMPD1):c.1763C>T (p.Thr588Met) rs35785620 0.01390
NM_000543.5(SMPD1):c.887G>A (p.Arg296Gln) rs35824453 0.01388
NM_000543.5(SMPD1):c.1625G>A (p.Arg542Gln) rs113467489 0.00629
NM_000543.5(SMPD1):c.719G>A (p.Arg240Gln) rs2634197 0.00622
NM_000543.5(SMPD1):c.1071C>T (p.Ala357=) rs72896268 0.00571
NM_000543.5(SMPD1):c.813T>C (p.Pro271=) rs61876771 0.00488
NM_000543.5(SMPD1):c.901G>A (p.Val301Ile) rs2723669 0.00374
NM_000543.5(SMPD1):c.99G>A (p.Met33Ile) rs142178073 0.00343
NM_000543.5(SMPD1):c.1561C>T (p.Leu521=) rs147258619 0.00316
NM_000543.5(SMPD1):c.1550A>T (p.Glu517Val) rs142787001 0.00284
NM_000543.5(SMPD1):c.1460C>T (p.Ala487Val) rs141641266 0.00282
NM_000543.5(SMPD1):c.441G>A (p.Val147=) rs148944108 0.00230
NM_000543.5(SMPD1):c.1589G>C (p.Gly530Ala) rs35122256 0.00150
NM_000543.5(SMPD1):c.1474G>A (p.Gly492Ser) rs144873307 0.00117
NM_000543.5(SMPD1):c.762G>A (p.Leu254=) rs143939609 0.00097
NM_000543.5(SMPD1):c.1091+9C>T rs143612450 0.00095
NM_000543.5(SMPD1):c.297C>G (p.Thr99=) rs146630228 0.00072
NM_000543.5(SMPD1):c.1598C>T (p.Pro533Leu) rs199915216 0.00070
NM_000543.5(SMPD1):c.689G>A (p.Arg230His) rs141387770 0.00064
NM_000543.5(SMPD1):c.1675G>A (p.Val559Ile) rs149939736 0.00051
NM_000543.5(SMPD1):c.319-17C>A rs148370501 0.00048
NM_000543.5(SMPD1):c.337C>T (p.Arg113Cys) rs140202512 0.00034
NM_000543.5(SMPD1):c.1599G>A (p.Pro533=) rs552841217 0.00019
NM_000543.5(SMPD1):c.103C>G (p.Leu35Val) rs201367689 0.00015
NM_000543.5(SMPD1):c.708G>A (p.Pro236=) rs374604948 0.00014
NM_000543.5(SMPD1):c.808G>A (p.Gly270Ser) rs202244080 0.00014
NM_000543.5(SMPD1):c.349G>A (p.Val117Met) rs202206564 0.00011
NM_000543.5(SMPD1):c.729C>T (p.Ala243=) rs149476159 0.00011
NM_000543.5(SMPD1):c.909A>G (p.Ala303=) rs201134693 0.00011
NM_000543.5(SMPD1):c.567A>G (p.Lys189=) rs750187574 0.00009
NM_000543.5(SMPD1):c.1133G>A (p.Arg378His) rs559088058 0.00007
NM_000543.5(SMPD1):c.1632C>T (p.Thr544=) rs201659696 0.00006
NM_000543.5(SMPD1):c.373C>T (p.Leu125=) rs370048730 0.00006
NM_000543.5(SMPD1):c.551C>T (p.Pro184Leu) rs760203204 0.00006
NM_000543.5(SMPD1):c.1426C>T (p.Arg476Trp) rs182812968 0.00005
NM_000543.5(SMPD1):c.475T>C (p.Cys159Arg) rs727504166 0.00004
NM_000543.5(SMPD1):c.557C>T (p.Pro186Leu) rs1057517195 0.00004
NM_000543.5(SMPD1):c.1498T>C (p.Tyr500His) rs771336819 0.00003
NM_000543.5(SMPD1):c.1587G>A (p.Pro529=) rs140770832 0.00003
NM_000543.5(SMPD1):c.533T>A (p.Ile178Asn) rs749780769 0.00003
NM_000543.5(SMPD1):c.730G>A (p.Gly244Arg) rs120074122 0.00003
NM_000543.5(SMPD1):c.739G>A (p.Gly247Ser) rs587779408 0.00003
NM_000543.5(SMPD1):c.911T>C (p.Leu304Pro) rs120074124 0.00003
NM_000543.5(SMPD1):c.940G>A (p.Val314Met) rs1228068212 0.00003
NM_000543.5(SMPD1):c.102C>G (p.Gly34=) rs889113421 0.00002
NM_000543.5(SMPD1):c.1054G>T (p.Glu352Ter) rs201550531 0.00002
NM_000543.5(SMPD1):c.1106A>G (p.Tyr369Cys) rs372287825 0.00002
NM_000543.5(SMPD1):c.1430C>T (p.Pro477Leu) rs753508874 0.00002
NM_000543.5(SMPD1):c.1492C>T (p.Arg498Cys) rs769904764 0.00002
NM_000543.5(SMPD1):c.234C>T (p.Pro78=) rs575601110 0.00002
NM_000543.5(SMPD1):c.1148A>G (p.Asn383Ser) rs776442314 0.00001
NM_000543.5(SMPD1):c.1202C>G (p.Pro401Arg) rs1206562843 0.00001
NM_000543.5(SMPD1):c.1268A>G (p.His423Arg) rs767492080 0.00001
NM_000543.5(SMPD1):c.1280A>G (p.His427Arg) rs794727629 0.00001
NM_000543.5(SMPD1):c.1299T>G (p.Cys433Trp) rs398123475 0.00001
NM_000543.5(SMPD1):c.1341-1G>A rs1057516854 0.00001
NM_000543.5(SMPD1):c.1341-9T>C rs528939343 0.00001
NM_000543.5(SMPD1):c.1343A>G (p.Tyr448Cys) rs747143343 0.00001
NM_000543.5(SMPD1):c.1427G>A (p.Arg476Gln) rs763566905 0.00001
NM_000543.5(SMPD1):c.1529C>T (p.Ser510Phe) rs200652683 0.00001
NM_000543.5(SMPD1):c.152A>T (p.Asp51Val) rs748589919 0.00001
NM_000543.5(SMPD1):c.1675_1676del (p.Val559fs) rs759389193 0.00001
NM_000543.5(SMPD1):c.1692C>T (p.Gly564=) rs369787650 0.00001
NM_000543.5(SMPD1):c.1730A>G (p.His577Arg) rs1554935669 0.00001
NM_000543.5(SMPD1):c.1801G>A (p.Ala601Thr) rs750433951 0.00001
NM_000543.5(SMPD1):c.1805G>A (p.Arg602His) rs370129081 0.00001
NM_000543.5(SMPD1):c.241C>T (p.Arg81Ter) rs868423827 0.00001
NM_000543.5(SMPD1):c.319-5T>C rs958654789 0.00001
NM_000543.5(SMPD1):c.502G>A (p.Gly168Arg) rs1847910654 0.00001
NM_000543.5(SMPD1):c.680T>C (p.Leu227Pro) rs764317969 0.00001
NM_000543.5(SMPD1):c.688C>T (p.Arg230Cys) rs989639224 0.00001
NM_000543.5(SMPD1):c.742G>A (p.Glu248Lys) rs200763423 0.00001
NM_000543.5(SMPD1):c.748A>C (p.Ser250Arg) rs750779804 0.00001
NM_000543.5(SMPD1):c.757G>C (p.Asp253His) rs398123479 0.00001
NM_000543.5(SMPD1):c.958A>G (p.Asn320Asp) rs779927660 0.00001
NM_000543.5(SMPD1):c.106_107insCGCTGG (p.Leu35_Val36insAlaLeu) rs1554933800
NM_000543.5(SMPD1):c.107_112del (p.Val36_Leu37del) rs775860642
NM_000543.5(SMPD1):c.107_124del (p.Val36_Leu41del) rs794726889
NM_000543.5(SMPD1):c.1088T>G (p.Leu363Arg) rs2134013368
NM_000543.5(SMPD1):c.108GCTGGC[4] (p.38AL[4]) rs3838786
NM_000543.5(SMPD1):c.108GCTGGC[5] (p.38AL[5]) rs3838786
NM_000543.5(SMPD1):c.108GCTGGC[7] (p.38AL[7]) rs3838786
NM_000543.5(SMPD1):c.108GCTGGC[8] (p.38AL[8]) rs3838786
NM_000543.5(SMPD1):c.108_109insGCG (p.Val36_Leu37insAla) rs775568984
NM_000543.5(SMPD1):c.1091+1G>A rs1847955457
NM_000543.5(SMPD1):c.1092-1G>C rs398123474
NM_000543.5(SMPD1):c.1101dup (p.Phe368fs) rs1422720020
NM_000543.5(SMPD1):c.1108dup (p.Ala370fs) rs1590743683
NM_000543.5(SMPD1):c.1111_1112del (p.Leu371fs) rs786204514
NM_000543.5(SMPD1):c.1145_1146del (p.Leu382fs) rs1057516432
NM_000543.5(SMPD1):c.1152G>A (p.Met384Ile) rs120074121
NM_000543.5(SMPD1):c.1171A>C (p.Asn391His) rs2134017443
NM_000543.5(SMPD1):c.1264-1G>C rs1057516454
NM_000543.5(SMPD1):c.1276G>A (p.Gly426Ser) rs1554935136
NM_000543.5(SMPD1):c.1340+2T>C rs1301641750
NM_000543.5(SMPD1):c.1363C>T (p.Gln455Ter) rs2134021058
NM_000543.5(SMPD1):c.1394T>C (p.Phe465Ser) rs1319643225
NM_000543.5(SMPD1):c.1406A>C (p.Tyr469Ser) rs267607074
NM_000543.5(SMPD1):c.148_151del (p.Ser50fs) rs281860676
NM_000543.5(SMPD1):c.1493G>A (p.Arg498His) rs120074117
NM_000543.5(SMPD1):c.151_154del (p.Asp51fs) rs1057516949
NM_000543.5(SMPD1):c.1547A>G (p.His516Arg) rs754979734
NM_000543.5(SMPD1):c.1548T>G (p.His516Gln) rs1590747902
NM_000543.5(SMPD1):c.1598C>A (p.Pro533Gln) rs199915216
NM_000543.5(SMPD1):c.1624C>T (p.Arg542Ter) rs398123478
NM_000543.5(SMPD1):c.1673T>C (p.Leu558Pro) rs875989836
NM_000543.5(SMPD1):c.167G>A (p.Trp56Ter) rs2134006149
NM_000543.5(SMPD1):c.1718G>C (p.Trp573Ser) rs2134024060
NM_000543.5(SMPD1):c.1735G>A (p.Gly579Ser) rs120074119
NM_000543.5(SMPD1):c.1783_1784del (p.Ala597fs) rs1437508852
NM_000543.5(SMPD1):c.1785_1786del (p.Ala597fs) rs1057516403
NM_000543.5(SMPD1):c.1817del (p.Pro606fs) rs1554935746
NM_000543.5(SMPD1):c.314T>C (p.Leu105Pro) rs751269562
NM_000543.5(SMPD1):c.354del (p.Ile119fs) rs727504165
NM_000543.5(SMPD1):c.362T>C (p.Leu121Pro) rs1554934109
NM_000543.5(SMPD1):c.488T>C (p.Leu163Pro) rs780134410
NM_000543.5(SMPD1):c.505dup (p.His169fs) rs781535659
NM_000543.5(SMPD1):c.518dup (p.Ser174fs) rs786204733
NM_000543.5(SMPD1):c.538_539del (p.Leu180fs) rs786204694
NM_000543.5(SMPD1):c.581del (p.Pro194fs) rs748165078
NM_000543.5(SMPD1):c.581dup (p.Ala195fs) rs748165078
NM_000543.5(SMPD1):c.597del (p.Val200fs) rs2493805239
NM_000543.5(SMPD1):c.682T>C (p.Cys228Arg) rs1564923612
NM_000543.5(SMPD1):c.698C>T (p.Ser233Phe) rs1847925080
NM_000543.5(SMPD1):c.730G>T (p.Gly244Ter) rs120074122
NM_000543.5(SMPD1):c.785_807del (p.Leu262fs) rs794727252
NM_000543.5(SMPD1):c.872G>A (p.Arg291His) rs1803161
NM_000543.5(SMPD1):c.955G>C (p.Gly319Arg) rs757934797
NM_000543.5(SMPD1):c.95G>A (p.Trp32Ter) rs1554933780
NM_000543.5(SMPD1):c.96G>A (p.Trp32Ter) rs786204506
NM_000543.5(SMPD1):c.995C>G (p.Pro332Arg) rs202081954
NM_000543.5(SMPD1):c.995C>T (p.Pro332Leu) rs202081954

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