ClinVar Miner

Variants from ClinGen Lysosomal Storage Disorder Variant Curation Expert Panel with conflicting interpretations

Location: United States  Primary collection method: curation
Minimum review status of the submission from ClinGen Lysosomal Storage Disorder Variant Curation Expert Panel: Collection method of the submission from ClinGen Lysosomal Storage Disorder Variant Curation Expert Panel:
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
28 88 0 145 11 1 45 185

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 submitters
ClinGen Lysosomal Storage Disorder Variant Curation Expert Panel pathogenic likely pathogenic uncertain significance likely benign benign other
pathogenic 0 85 3 0 0 0
likely pathogenic 50 0 17 0 0 0
uncertain significance 12 20 0 6 1 0
likely benign 0 0 4 0 5 0
benign 0 0 1 5 0 1

Submitter to submitter summary #

Total submitters: 28
Download table as spreadsheet
Submitter 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
Counsyl 0 46 0 66 0 0 11 77
Invitae 0 157 0 51 7 1 18 77
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard 0 69 0 25 2 0 7 34
Baylor Genetics 0 108 0 19 0 0 8 27
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 74 0 18 0 0 5 23
Genome-Nilou Lab 0 36 0 6 2 0 10 18
Natera, Inc. 0 88 0 6 2 0 7 15
Fulgent Genetics, Fulgent Genetics 0 57 0 9 1 0 1 11
Illumina Laboratory Services, Illumina 0 23 0 3 4 0 0 7
Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital 0 4 0 5 0 0 1 6
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 0 17 0 1 1 0 1 3
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics 0 3 0 2 0 0 1 3
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center 0 3 0 0 0 0 2 2
Centre for Mendelian Genomics, University Medical Centre Ljubljana 0 1 0 2 0 0 0 2
Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City 0 0 0 1 0 0 1 2
Department of Pediatrics, Division of Medical Genetics, Faculty of Medicine Ramathibodi Hospital, Mahidol University 0 1 0 1 0 0 1 2
Myriad Genetics, Inc. 0 10 0 2 0 0 0 2
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 6 0 1 0 0 0 1
Centogene AG - the Rare Disease Company 0 1 0 0 0 0 1 1
Knight Diagnostic Laboratories, Oregon Health and Sciences University 0 2 0 1 0 0 0 1
Hadassah Hebrew University Medical Center 0 0 0 1 0 0 0 1
SIB Swiss Institute of Bioinformatics 0 0 0 1 0 0 0 1
Tehran Medical Genetics Laboratory 0 0 0 1 0 0 0 1
Laboratory of Medical Genetics, National & Kapodistrian University of Athens 0 2 0 1 0 0 0 1
Biochemical Genetics Department, Cyprus Institute of Neurology and Genetics 0 0 0 0 0 0 1 1
NxGen MDx 0 1 0 0 0 0 1 1
Molecular Therapies Laboratory, Murdoch University 0 4 0 1 0 0 0 1
Beijing Key Laboratry for Genetics of Birth Defects, Beijing Children's Hospital 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 185
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000152.5(GAA):c.668G>A (p.Arg223His) rs1042395 0.65662
NM_000152.5(GAA):c.271G>A (p.Asp91Asn) rs1800299 0.02215
NM_000152.5(GAA):c.852G>A (p.Ala284=) rs142626724 0.00638
NM_000152.5(GAA):c.1552-13G>A rs111261964 0.00276
NM_000152.5(GAA):c.676C>G (p.Leu226Val) rs113085339 0.00193
NM_000152.5(GAA):c.258C>A (p.Pro86=) rs146615896 0.00170
NM_000152.5(GAA):c.726G>A (p.Ala242=) rs148578399 0.00101
NM_000152.5(GAA):c.2417C>T (p.Thr806Met) rs139850074 0.00056
NM_000152.5(GAA):c.841C>T (p.Arg281Trp) rs142967546 0.00033
NM_000152.5(GAA):c.1286A>G (p.Gln429Arg) rs200294882 0.00026
NM_000152.5(GAA):c.2152G>A (p.Val718Ile) rs141017311 0.00021
NM_000152.5(GAA):c.131G>T (p.Gly44Val) rs550609502 0.00017
NM_000152.5(GAA):c.1332T>C (p.Pro444=) rs200007324 0.00015
NM_000152.5(GAA):c.1979G>A (p.Arg660His) rs374143224 0.00009
NM_000152.5(GAA):c.1194+3G>C rs368539333 0.00008
NM_000152.5(GAA):c.1552-3C>G rs375470378 0.00008
NM_000152.5(GAA):c.853C>T (p.Pro285Ser) rs886042086 0.00008
NM_000152.5(GAA):c.1048G>A (p.Val350Met) rs200412003 0.00007
NM_000152.5(GAA):c.1504A>G (p.Met502Val) rs376067362 0.00007
NM_000152.5(GAA):c.658G>T (p.Val220Leu) rs530478036 0.00007
NM_000152.5(GAA):c.266G>A (p.Arg89His) rs200586324 0.00006
NM_000152.5(GAA):c.655G>A (p.Gly219Arg) rs370950728 0.00006
NM_000152.5(GAA):c.953T>C (p.Met318Thr) rs121907936 0.00006
NM_000152.5(GAA):c.1409A>C (p.Asn470Thr) rs144155165 0.00005
NM_000152.5(GAA):c.510C>T (p.Asp170=) rs564758226 0.00005
NM_000152.5(GAA):c.1309C>T (p.Arg437Cys) rs770610356 0.00004
NM_000152.5(GAA):c.1478C>T (p.Pro493Leu) rs148842275 0.00004
NM_000152.5(GAA):c.1548G>A (p.Trp516Ter) rs140826989 0.00004
NM_000152.5(GAA):c.1827del (p.Arg608_Tyr609insTer) rs781088002 0.00004
NM_000152.5(GAA):c.1828G>A (p.Ala610Thr) rs144731405 0.00004
NM_000152.5(GAA):c.781G>A (p.Ala261Thr) rs543360994 0.00004
NM_000152.5(GAA):c.784G>A (p.Glu262Lys) rs201896815 0.00004
NM_000152.5(GAA):c.1316T>A (p.Met439Lys) rs747610090 0.00003
NM_000152.5(GAA):c.1326+1G>A rs1205507761 0.00003
NM_000152.5(GAA):c.1941C>G (p.Cys647Trp) rs776948121 0.00003
NM_000152.5(GAA):c.2105G>A (p.Arg702His) rs398123172 0.00003
NM_000152.5(GAA):c.2173C>T (p.Arg725Trp) rs121907938 0.00003
NM_000152.5(GAA):c.2297A>G (p.Tyr766Cys) rs144016984 0.00003
NM_000152.5(GAA):c.2455C>T (p.Arg819Trp) rs61736895 0.00003
NM_000152.5(GAA):c.2608C>T (p.Arg870Ter) rs780321415 0.00003
NM_000152.5(GAA):c.2799+4A>G rs778032599 0.00003
NM_000152.5(GAA):c.307T>G (p.Cys103Gly) rs398123174 0.00003
NM_000152.5(GAA):c.546G>A (p.Thr182=) rs143523371 0.00003
NM_000152.5(GAA):c.1076-22T>G rs762260678 0.00002
NM_000152.5(GAA):c.1441T>C (p.Trp481Arg) rs772883420 0.00002
NM_000152.5(GAA):c.1710C>G (p.Asn570Lys) rs765362308 0.00002
NM_000152.5(GAA):c.1735G>A (p.Glu579Lys) rs991082382 0.00002
NM_000152.5(GAA):c.1831G>A (p.Gly611Ser) rs1278340100 0.00002
NM_000152.5(GAA):c.1912G>T (p.Gly638Trp) rs757617999 0.00002
NM_000152.5(GAA):c.2015G>A (p.Arg672Gln) rs778418246 0.00002
NM_000152.5(GAA):c.2668G>C (p.Val890Leu) rs377286472 0.00002
NM_000152.5(GAA):c.868A>G (p.Asn290Asp) rs552929702 0.00002
NM_000152.5(GAA):c.971C>T (p.Pro324Leu) rs750030887 0.00002
NM_000152.5(GAA):c.1082C>T (p.Pro361Leu) rs755253527 0.00001
NM_000152.5(GAA):c.1123C>T (p.Arg375Cys) rs372486238 0.00001
NM_000152.5(GAA):c.1222A>G (p.Met408Val) rs560575383 0.00001
NM_000152.5(GAA):c.1292_1295dup (p.Gln433fs) rs996798292 0.00001
NM_000152.5(GAA):c.1327-2A>G rs1410829147 0.00001
NM_000152.5(GAA):c.1402A>T (p.Ile468Phe) rs886043148 0.00001
NM_000152.5(GAA):c.1411_1414del (p.Glu471fs) rs770276275 0.00001
NM_000152.5(GAA):c.1447G>A (p.Gly483Arg) rs770590394 0.00001
NM_000152.5(GAA):c.1537G>A (p.Asp513Asn) rs748047271 0.00001
NM_000152.5(GAA):c.1556T>C (p.Met519Thr) rs786204720 0.00001
NM_000152.5(GAA):c.1626C>G (p.Pro542=) rs947585663 0.00001
NM_000152.5(GAA):c.172C>T (p.Gln58Ter) rs201185475 0.00001
NM_000152.5(GAA):c.1796C>A (p.Ser599Tyr) rs753505203 0.00001
NM_000152.5(GAA):c.1799G>A (p.Arg600His) rs377544304 0.00001
NM_000152.5(GAA):c.1802C>T (p.Ser601Leu) rs374470794 0.00001
NM_000152.5(GAA):c.1820G>A (p.Gly607Asp) rs1393386120 0.00001
NM_000152.5(GAA):c.1826dup (p.Tyr609Ter) rs786204727 0.00001
NM_000152.5(GAA):c.1843G>A (p.Gly615Arg) rs549029029 0.00001
NM_000152.5(GAA):c.1942G>A (p.Gly648Ser) rs536906561 0.00001
NM_000152.5(GAA):c.1962_1964del (p.Glu656del) rs1030961946 0.00001
NM_000152.5(GAA):c.2014C>T (p.Arg672Trp) rs757111744 0.00001
NM_000152.5(GAA):c.2174G>A (p.Arg725Gln) rs577042191 0.00001
NM_000152.5(GAA):c.265C>T (p.Arg89Cys) rs534192892 0.00001
NM_000152.5(GAA):c.2706del (p.Lys903fs) rs1428358278 0.00001
NM_000152.5(GAA):c.2783A>G (p.Tyr928Cys) rs1403885484 0.00001
NM_000152.5(GAA):c.281_282del (p.Pro94fs) rs1057516503 0.00001
NM_000152.5(GAA):c.316C>T (p.Arg106Cys) rs915675670 0.00001
NM_000152.5(GAA):c.365del (p.Met122fs) rs786204661 0.00001
NM_000152.5(GAA):c.670C>T (p.Arg224Trp) rs757700700 0.00001
NM_000152.5(GAA):c.671G>A (p.Arg224Gln) rs200210219 0.00001
NM_000152.5(GAA):c.871C>T (p.Leu291Phe) rs773417785 0.00001
NM_000152.5(GAA):c.-32-3C>A rs1055945806
NM_000152.5(GAA):c.1003G>A (p.Gly335Arg) rs202095215
NM_000152.5(GAA):c.1030_1031del (p.Gly344fs) rs1567829962
NM_000152.5(GAA):c.1051del (p.Val351fs) rs786204507
NM_000152.5(GAA):c.1062C>A (p.Tyr354Ter) rs1064796703
NM_000152.5(GAA):c.1082C>G (p.Pro361Arg) rs755253527
NM_000152.5(GAA):c.1099T>C (p.Trp367Arg) rs1555600061
NM_000152.5(GAA):c.1124G>T (p.Arg375Leu) rs142752477
NM_000152.5(GAA):c.1128_1129delinsC (p.Trp376fs) rs786204646
NM_000152.5(GAA):c.1143del (p.Ala382fs) rs757458607
NM_000152.5(GAA):c.1156C>T (p.Gln386Ter) rs786204517
NM_000152.5(GAA):c.1190C>T (p.Pro397Leu) rs776008078
NM_000152.5(GAA):c.1192dup (p.Leu398fs) rs1057516546
NM_000152.5(GAA):c.1193del (p.Leu398fs) rs1057517286
NM_000152.5(GAA):c.1317GAT[1] (p.Met440del) rs1555600235
NM_000152.5(GAA):c.1346C>T (p.Ser449Leu) rs753483808
NM_000152.5(GAA):c.1375G>A (p.Asp459Asn) rs535644999
NM_000152.5(GAA):c.1385T>C (p.Leu462Pro) rs2143866454
NM_000152.5(GAA):c.1408_1410del (p.Asn470del) rs748893499
NM_000152.5(GAA):c.1431del (p.Ile477fs) rs1598580364
NM_000152.5(GAA):c.1437+1G>A rs1555600575
NM_000152.5(GAA):c.1438-1G>C rs147804176
NM_000152.5(GAA):c.1438-2A>G rs1555600730
NM_000152.5(GAA):c.1445C>G (p.Pro482Arg) rs2039212985
NM_000152.5(GAA):c.1445C>T (p.Pro482Leu) rs2039212985
NM_000152.5(GAA):c.1465G>A (p.Asp489Asn) rs398123169
NM_000152.5(GAA):c.1496G>A (p.Trp499Ter) rs766680292
NM_000152.5(GAA):c.1538A>G (p.Asp513Gly) rs1598581682
NM_000152.5(GAA):c.1564C>G (p.Pro522Ala) rs892129065
NM_000152.5(GAA):c.1579_1580del (p.Arg527fs) rs1291214871
NM_000152.5(GAA):c.1669A>T (p.Ile557Phe) rs747150965
NM_000152.5(GAA):c.1687C>T (p.Gln563Ter) rs1057516426
NM_000152.5(GAA):c.1692del (p.Leu565fs) rs1555601234
NM_000152.5(GAA):c.169C>T (p.Gln57Ter) rs1057516251
NM_000152.5(GAA):c.1716C>G (p.His572Gln) rs772962666
NM_000152.5(GAA):c.1781G>A (p.Arg594His) rs775450536
NM_000152.5(GAA):c.1824_1828dup (p.Ala610fs) rs1057516826
NM_000152.5(GAA):c.1832G>A (p.Gly611Asp) rs1057517105
NM_000152.5(GAA):c.1841C>A (p.Thr614Lys) rs369531647
NM_000152.5(GAA):c.1841C>T (p.Thr614Met) rs369531647
NM_000152.5(GAA):c.1847dup (p.Asp616fs) rs1475559733
NM_000152.5(GAA):c.1857C>G (p.Ser619Arg) rs914396317
NM_000152.5(GAA):c.1905C>A (p.Asn635Lys) rs1414146587
NM_000152.5(GAA):c.1933G>A (p.Asp645Asn) rs368438393
NM_000152.5(GAA):c.1940G>T (p.Cys647Phe) rs1265892085
NM_000152.5(GAA):c.1941C>A (p.Cys647Ter) rs776948121
NM_000152.5(GAA):c.1951_1952delinsT (p.Gly651fs) rs1567835781
NM_000152.5(GAA):c.1952del (p.Gly651fs) rs1567835775
NM_000152.5(GAA):c.1978C>T (p.Arg660Cys) rs759518659
NM_000152.5(GAA):c.1A>T (p.Met1Leu) rs786204467
NM_000152.5(GAA):c.2003A>G (p.Tyr668Cys) rs1555601633
NM_000152.5(GAA):c.2105G>C (p.Arg702Pro) rs398123172
NM_000152.5(GAA):c.2132_2133delinsGG (p.Thr711Arg) rs1555601773
NM_000152.5(GAA):c.2136_2137del (p.Phe713fs) rs1555601780
NM_000152.5(GAA):c.2140del (p.His714fs) rs786204549
NM_000152.5(GAA):c.2185del (p.Leu729fs) rs1057516581
NM_000152.5(GAA):c.2214G>A (p.Trp738Ter) rs1057516328
NM_000152.5(GAA):c.2238G>A (p.Trp746Ter) rs1800312
NM_000152.5(GAA):c.2238G>C (p.Trp746Cys) rs1800312
NM_000152.5(GAA):c.2242G>T (p.Glu748Ter) rs1057516363
NM_000152.5(GAA):c.2242del (p.Glu748fs) rs777275355
NM_000152.5(GAA):c.2242dup (p.Glu748fs) rs777275355
NM_000152.5(GAA):c.2281delinsAT (p.Ala761fs) rs1057516924
NM_000152.5(GAA):c.2297A>C (p.Tyr766Ser) rs144016984
NM_000152.5(GAA):c.2300del (p.Phe767fs) rs1555602692
NM_000152.5(GAA):c.2314T>C (p.Trp772Arg) rs1555602703
NM_000152.5(GAA):c.2367dup (p.Pro790fs) rs1555602860
NM_000152.5(GAA):c.2383G>T (p.Glu795Ter) rs886043882
NM_000152.5(GAA):c.241C>T (p.Gln81Ter) rs1555598687
NM_000152.5(GAA):c.2456G>C (p.Arg819Pro) rs374687883
NM_000152.5(GAA):c.2501_2502del (p.Thr834fs) rs886043343
NM_000152.5(GAA):c.2544del (p.Lys849fs) rs398123173
NM_000152.5(GAA):c.258del (p.Asn87fs) rs761317813
NM_000152.5(GAA):c.2646+2T>A rs786204561
NM_000152.5(GAA):c.2704C>T (p.Gln902Ter) rs1057516341
NM_000152.5(GAA):c.2740C>T (p.Gln914Ter) rs1555603264
NM_000152.5(GAA):c.276C>A (p.Cys92Ter) rs1232001857
NM_000152.5(GAA):c.2799+2C>A rs1555603318
NM_000152.5(GAA):c.2815_2816del (p.Val939fs) rs763359208
NM_000152.5(GAA):c.342del (p.Lys114fs) rs1555598796
NM_000152.5(GAA):c.343C>T (p.Gln115Ter) rs786204614
NM_000152.5(GAA):c.352C>T (p.Gln118Ter) rs1555598800
NM_000152.5(GAA):c.437del (p.Met146fs) rs1555598869
NM_000152.5(GAA):c.471del (p.Thr158fs) rs1057517320
NM_000152.5(GAA):c.525_526del (p.Asn177fs) rs767882689
NM_000152.5(GAA):c.546+5G>T rs756024023
NM_000152.5(GAA):c.546G>T (p.Thr182=) rs143523371
NM_000152.5(GAA):c.573C>A (p.Tyr191Ter) rs376229714
NM_000152.5(GAA):c.688G>A (p.Val230Met) rs145866792
NM_000152.5(GAA):c.710C>T (p.Ala237Val) rs121907944
NM_000152.5(GAA):c.716del (p.Leu239fs) rs1555599594
NM_000152.5(GAA):c.736del (p.Leu246fs) rs886043920
NM_000152.5(GAA):c.755dup (p.Pro253fs) rs1555599619
NM_000152.5(GAA):c.766_785delinsC (p.Tyr256fs) rs786204532
NM_000152.5(GAA):c.768dup (p.Ile257fs) rs1555599644
NM_000152.5(GAA):c.796C>T (p.Pro266Ser) rs1555599667
NM_000152.5(GAA):c.806_830del (p.Leu269fs) rs1598575231
NM_000152.5(GAA):c.858+17_858+23del rs1555599723
NM_000152.5(GAA):c.896T>G (p.Leu299Arg) rs121907940
NM_000152.5(GAA):c.953T>A (p.Met318Lys) rs121907936
NM_000152.5(GAA):c.989G>A (p.Trp330Ter) rs1555599960

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