ClinVar Miner

Variants with conflicting interpretations between ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories and Genome-Nilou Lab

Minimum review status of the submission from ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories: Collection method of the submission from ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories:
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
1820 433 0 59 7 0 5 71

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 11 0 0 0
likely pathogenic 5 0 2 0 0
uncertain significance 0 3 0 3 0
likely benign 0 0 3 0 21
benign 0 0 1 22 0

All variants with conflicting interpretations #

Total variants: 71
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000053.4(ATP7B):c.3903+6C>T rs2282057 0.53754
NM_000053.4(ATP7B):c.1216T>G (p.Ser406Ala) rs1801243 0.41549
NM_000155.4(GALT):c.940A>G (p.Asn314Asp) rs2070074 0.07150
NM_000053.4(ATP7B):c.3620A>G (p.His1207Arg) rs7334118 0.02828
NM_001232.4(CASQ2):c.731A>G (p.His244Arg) rs28730716 0.02511
NM_001232.4(CASQ2):c.1005T>C (p.Asn335=) rs28730712 0.02116
NM_000098.3(CPT2):c.1055T>G (p.Phe352Cys) rs2229291 0.01469
NM_000037.4(ANK1):c.654C>A (p.Asn218Lys) rs61735313 0.01280
NM_002506.3(NGF):c.239G>A (p.Arg80Gln) rs11466111 0.01173
NM_000289.6(PFKM):c.2087G>A (p.Arg696His) rs41291971 0.01088
NM_002529.4(NTRK1):c.53G>A (p.Gly18Glu) rs1007211 0.00957
NM_000069.3(CACNA1S):c.1817G>A (p.Ser606Asn) rs142356235 0.00873
NM_001918.5(DBT):c.724T>C (p.Ser242Pro) rs146249007 0.00864
NM_022356.4(P3H1):c.2055+70G>T rs115690038 0.00864
NM_014915.3(ANKRD26):c.3655G>A (p.Val1219Ile) rs146819984 0.00781
NM_001365088.1(SLC12A6):c.318C>T (p.Asp106=) rs116086579 0.00575
NM_006939.4(SOS2):c.2014C>A (p.Leu672Ile) rs34139502 0.00561
NM_000255.4(MMUT):c.1629C>T (p.Ser543=) rs150642856 0.00479
NM_000108.5(DLD):c.543A>T (p.Ile181=) rs61749952 0.00461
NM_006939.4(SOS2):c.572C>G (p.Pro191Arg) rs72681869 0.00421
NM_000053.4(ATP7B):c.3369G>A (p.Pro1123=) rs61733679 0.00362
NM_000152.5(GAA):c.447G>A (p.Thr149=) rs2289536 0.00362
NM_003060.4(SLC22A5):c.1463G>A (p.Arg488His) rs28383481 0.00347
NM_000053.4(ATP7B):c.3557-6C>T rs140708492 0.00314
NM_000053.4(ATP7B):c.4301C>T (p.Thr1434Met) rs60986317 0.00282
NM_000037.4(ANK1):c.5097-34C>T rs185434561 0.00261
NM_000037.4(ANK1):c.981C>T (p.Tyr327=) rs61758867 0.00253
NM_001127671.2(LIFR):c.2447A>G (p.Asp816Gly) rs74856317 0.00245
NM_014915.3(ANKRD26):c.2679A>G (p.Gln893=) rs61730098 0.00215
NM_000053.4(ATP7B):c.628A>G (p.Ile210Val) rs61733680 0.00204
NM_000053.4(ATP7B):c.3889G>A (p.Val1297Ile) rs148399850 0.00192
NM_002529.4(NTRK1):c.1354+18A>T rs73004759 0.00164
NM_000053.4(ATP7B):c.2972C>T (p.Thr991Met) rs41292782 0.00155
NM_000053.4(ATP7B):c.1620C>T (p.Leu540=) rs145798966 0.00150
NM_005751.5(AKAP9):c.10197T>C (p.Thr3399=) rs143627839 0.00148
NM_000037.4(ANK1):c.5395-1162C>A rs145094714 0.00138
NM_000053.4(ATP7B):c.2605G>A (p.Gly869Arg) rs191312027 0.00101
NM_000053.4(ATP7B):c.2174G>A (p.Arg725Lys) rs115227204 0.00086
NM_006939.4(SOS2):c.549G>C (p.Leu183Phe) rs137961578 0.00083
NM_002225.5(IVD):c.891G>A (p.Ala297=) rs138427412 0.00069
NM_003060.4(SLC22A5):c.1441G>A (p.Val481Ile) rs11568513 0.00061
NM_000037.4(ANK1):c.1467G>A (p.Leu489=) rs148165519 0.00057
NM_003060.4(SLC22A5):c.136C>T (p.Pro46Ser) rs202088921 0.00052
NM_006939.4(SOS2):c.1071A>G (p.Gln357=) rs111961549 0.00046
NM_000053.4(ATP7B):c.2544C>T (p.Gly848=) rs200996053 0.00045
NM_000053.4(ATP7B):c.122A>G (p.Asn41Ser) rs201738967 0.00025
NM_001182.5(ALDH7A1):c.1279G>C (p.Glu427Gln) rs121912707 0.00024
NM_006939.4(SOS2):c.2712A>G (p.Glu904=) rs143332839 0.00020
NM_003060.4(SLC22A5):c.695C>T (p.Thr232Met) rs114269482 0.00018
NM_001130438.3(SPTAN1):c.7161-8G>A rs202180736 0.00014
NM_006939.4(SOS2):c.702G>A (p.Leu234=) rs200208472 0.00012
NM_000053.4(ATP7B):c.3859G>A (p.Gly1287Ser) rs762866453 0.00009
NM_000152.5(GAA):c.1552-3C>G rs375470378 0.00008
NM_000053.4(ATP7B):c.3796G>A (p.Gly1266Arg) rs121907992 0.00006
NM_000152.5(GAA):c.1356C>T (p.Ala452=) rs757893858 0.00006
NM_003060.4(SLC22A5):c.1193C>T (p.Pro398Leu) rs144547521 0.00006
NM_000053.4(ATP7B):c.2310C>G (p.Leu770=) rs398123136 0.00005
NM_000053.4(ATP7B):c.3316G>A (p.Val1106Ile) rs541208827 0.00005
NM_000053.4(ATP7B):c.4039G>A (p.Gly1347Ser) rs587783318 0.00004
NM_003060.4(SLC22A5):c.680G>A (p.Arg227His) rs185551386 0.00004
NM_000053.4(ATP7B):c.2804C>T (p.Thr935Met) rs750019452 0.00003
NM_000152.5(GAA):c.2668G>C (p.Val890Leu) rs377286472 0.00002
NM_000053.4(ATP7B):c.2383C>T (p.Leu795Phe) rs751710854 0.00001
NM_000053.4(ATP7B):c.3556G>A (p.Gly1186Ser) rs786204547 0.00001
NM_000053.4(ATP7B):c.3190G>A (p.Glu1064Lys) rs376910645
NM_000053.4(ATP7B):c.3203A>G (p.Glu1068Gly) rs1555286478
NM_000069.3(CACNA1S):c.773G>A (p.Gly258Asp) rs35534614
NM_003060.4(SLC22A5):c.248G>T (p.Arg83Leu) rs72552726
NM_003060.4(SLC22A5):c.505C>T (p.Arg169Trp) rs121908890
NM_006912.6(RIT1):c.246T>G (p.Phe82Leu) rs730881014
NM_006939.4(SOS2):c.2057+19_2057+20del rs111970905

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