ClinVar Miner

Variants with conflicting interpretations studied for Niemann-Pick disease, type A

Coded as:
Minimum review status of the submission for Niemann-Pick disease, type A: Collection method of the submission for Niemann-Pick disease, type A:
Minimum review status of the other submission: Collection method of the other submission:
Minimum conflict level:
ClinVar version:

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
196 48 0 48 11 0 19 75

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.

All conditions
Niemann-Pick disease, type A pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 44 5 1 0
likely pathogenic 44 0 15 0 0
uncertain significance 5 15 0 10 2
likely benign 1 0 10 0 4
benign 0 0 2 4 0

Condition to condition summary #

Total conditions: 1
Download table as spreadsheet
Condition 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
Niemann-Pick disease, type A 196 48 0 48 11 0 19 75

All variants with conflicting interpretations #

Total variants: 75
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HGVS dbSNP gnomAD frequency
NM_000543.5(SMPD1):c.1625G>A (p.Arg542Gln) rs113467489 0.00629
NM_000543.5(SMPD1):c.1071C>T (p.Ala357=) rs72896268 0.00571
NM_000543.5(SMPD1):c.813T>C (p.Pro271=) rs61876771 0.00500
NM_000543.5(SMPD1):c.1561C>T (p.Leu521=) rs147258619 0.00349
NM_000543.5(SMPD1):c.1460C>T (p.Ala487Val) rs141641266 0.00282
NM_000543.5(SMPD1):c.441G>A (p.Val147=) rs148944108 0.00241
NM_000543.5(SMPD1):c.1589G>C (p.Gly530Ala) rs35122256 0.00150
NM_000543.5(SMPD1):c.1091+9C>T rs143612450 0.00103
NM_000543.5(SMPD1):c.689G>A (p.Arg230His) rs141387770 0.00071
NM_000543.5(SMPD1):c.349G>A (p.Val117Met) rs202206564 0.00011
NM_000543.5(SMPD1):c.909A>G (p.Ala303=) rs201134693 0.00011
NM_000543.5(SMPD1):c.1133G>A (p.Arg378His) rs559088058 0.00006
NM_000543.5(SMPD1):c.1632C>T (p.Thr544=) rs201659696 0.00006
NM_000543.5(SMPD1):c.1426C>T (p.Arg476Trp) rs182812968 0.00004
NM_000543.5(SMPD1):c.1599G>A (p.Pro533=) rs552841217 0.00004
NM_000543.5(SMPD1):c.475T>C (p.Cys159Arg) rs727504166 0.00004
NM_000543.5(SMPD1):c.533T>A (p.Ile178Asn) rs749780769 0.00004
NM_000543.5(SMPD1):c.1498T>C (p.Tyr500His) rs771336819 0.00003
NM_000543.5(SMPD1):c.739G>A (p.Gly247Ser) rs587779408 0.00003
NM_000543.5(SMPD1):c.940G>A (p.Val314Met) rs1228068212 0.00003
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.757G>C (p.Asp253His) rs398123479 0.00002
NM_000543.5(SMPD1):c.1148A>G (p.Asn383Ser) rs776442314 0.00001
NM_000543.5(SMPD1):c.1280A>G (p.His427Arg) rs794727629 0.00001
NM_000543.5(SMPD1):c.1341-1G>A rs1057516854 0.00001
NM_000543.5(SMPD1):c.1343A>G (p.Tyr448Cys) rs747143343 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.1730A>G (p.His577Arg) rs1554935669 0.00001
NM_000543.5(SMPD1):c.1735G>A (p.Gly579Ser) rs120074119 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.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.83C>T (p.Pro28Leu) rs556155962 0.00001
NM_000543.5(SMPD1):c.958A>G (p.Asn320Asp) rs779927660 0.00001
NM_000543.5(SMPD1):c.1092-1G>C rs398123474
NM_000543.5(SMPD1):c.1101dup (p.Phe368fs) rs1422720020
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.1276G>A (p.Gly426Ser) rs1554935136
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.1598C>A (p.Pro533Gln) rs199915216
NM_000543.5(SMPD1):c.1624C>T (p.Arg542Ter) rs398123478
NM_000543.5(SMPD1):c.1718G>C (p.Trp573Ser) rs2134024060
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.56del (p.Gln19fs) rs1554933746
NM_000543.5(SMPD1):c.581dup (p.Ala195fs) rs748165078
NM_000543.5(SMPD1):c.61C>T (p.Gln21Ter) rs1554933751
NM_000543.5(SMPD1):c.682T>C (p.Cys228Arg) rs1564923612
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

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