ClinVar Miner

Variants from Department of Clinical Pathology, School of Medicine, Fujita Health University with conflicting interpretations

Location: Japan  Primary collection method: research
Minimum review status of the submission from Department of Clinical Pathology, School of Medicine, Fujita Health University: Collection method of the submission from Department of Clinical Pathology, School of Medicine, Fujita Health University:
Minimum review status of the other submission: Collection method of the other submission:
Minimum conflict level:

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
507 18 0 3 38 0 6 46

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
Department of Clinical Pathology, School of Medicine, Fujita Health University likely pathogenic uncertain significance
pathogenic 3 5
likely benign 1 38

Submitter to submitter summary #

Total submitters: 18
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
Ambry Genetics 0 4 0 0 19 0 0 19
GeneDx 0 5 0 1 8 0 1 10
Labcorp Genetics (formerly Invitae), Labcorp 0 7 0 1 7 0 2 10
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 1 0 0 3 0 2 5
Revvity Omics, Revvity 0 0 0 1 2 0 0 3
Athena Diagnostics 0 0 0 0 2 0 0 2
CeGaT Center for Human Genetics Tuebingen 0 5 0 0 1 0 1 2
PreventionGenetics, part of Exact Sciences 0 4 0 0 1 0 1 2
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 0 0 0 0 1 0 0 1
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital 0 0 0 0 0 0 1 1
Department of Pathology and Laboratory Medicine, Sinai Health System 0 0 0 0 1 0 0 1
Eurofins Ntd Llc (ga) 0 0 0 0 1 0 0 1
Foulkes Cancer Genetics LDI, Lady Davis Institute for Medical Research 0 0 0 0 1 0 0 1
Genetic Services Laboratory, University of Chicago 0 0 0 0 0 0 1 1
Institute of Human Genetics, University of Leipzig Medical Center 0 0 0 0 1 0 0 1
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 0 0 0 1 0 0 1
Mendelics 0 1 0 0 1 0 0 1
Quest Diagnostics Nichols Institute San Juan Capistrano 0 1 0 0 1 0 0 1

All variants with conflicting interpretations #

Total variants: 46
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_001136506.2(SLC22A24):c.268C>T (p.Arg90Cys) rs556942414 0.00029
NM_173352.4(KRT78):c.1112C>T (p.Ala371Val) rs144560690 0.00019
NM_152701.5(ABCA13):c.12074G>A (p.Arg4025His) rs200382482 0.00015
NM_018136.5(ASPM):c.5137C>T (p.Arg1713Cys) rs143911853 0.00011
NM_005529.7(HSPG2):c.5815G>A (p.Ala1939Thr) rs145474376 0.00010
NM_001080467.3(MYO5B):c.3296G>A (p.Arg1099Gln) rs377018425 0.00009
NM_001267550.2(TTN):c.89947G>A (p.Val29983Met) rs397517746 0.00009
NM_013385.5(CYTH4):c.40G>A (p.Gly14Arg) rs201471657 0.00006
NM_022552.5(DNMT3A):c.2711C>T (p.Pro904Leu) rs149095705 0.00006
NM_001077653.2(TBX20):c.1321G>A (p.Ala441Thr) rs750770210 0.00005
NM_006035.4(CDC42BPB):c.1552C>T (p.Arg518Cys) rs200810382 0.00004
NM_152743.4(BRAT1):c.1702G>A (p.Ala568Thr) rs141709461 0.00004
NM_001286577.2(C2CD3):c.2750G>A (p.Arg917His) rs765019392 0.00003
NM_007256.5(SLCO2B1):c.257C>T (p.Thr86Met) rs140953109 0.00003
NM_033026.6(PCLO):c.13580G>C (p.Ser4527Thr) rs377297010 0.00003
NM_004882.4(CIRSR):c.1226G>A (p.Arg409Gln) rs769148227 0.00002
NM_005440.5(RND2):c.568C>T (p.Arg190Cys) rs376927688 0.00002
NM_183375.5(PRSS48):c.79C>T (p.Arg27Cys) rs776335390 0.00002
NM_198148.3(CPXM2):c.913C>T (p.Arg305Trp) rs372846460 0.00002
NM_000059.4(BRCA2):c.1244A>G (p.His415Arg) rs80358417 0.00001
NM_001083619.3(GRIA2):c.413G>A (p.Ser138Asn) rs761500896 0.00001
NM_001127208.3(TET2):c.2746C>T (p.Gln916Ter) rs780710758 0.00001
NM_001127208.3(TET2):c.3409+1G>A rs772634266 0.00001
NM_001191057.4(PDE1C):c.134G>A (p.Arg45Gln) rs775258741 0.00001
NM_001308210.2(TSHZ1):c.2395G>A (p.Asp799Asn) rs1020952592 0.00001
NM_001987.5(ETV6):c.146G>A (p.Arg49His) rs1007158603 0.00001
NM_012254.3(SLC27A5):c.1606G>T (p.Val536Leu) rs751110550 0.00001
NM_016146.6(TRAPPC4):c.7A>G (p.Ile3Val) rs781822453 0.00001
NM_018006.5(TRMU):c.220G>A (p.Val74Ile) rs956018032 0.00001
NM_139276.3(STAT3):c.1919A>T (p.Tyr640Phe) rs769031989 0.00001
NM_139276.3(STAT3):c.1981G>T (p.Asp661Tyr) rs747639500 0.00001
NM_182521.3(ZSWIM2):c.139G>A (p.Glu47Lys) rs1422325092 0.00001
NM_000552.5(VWF):c.3797C>A (p.Pro1266Gln) rs61749370
NM_001017425.3(KCNK2):c.82G>A (p.Ala28Thr) rs368923002
NM_001017970.3(TMEM30B):c.836C>T (p.Pro279Leu) rs2503976579
NM_001127208.3(TET2):c.5618T>C (p.Ile1873Thr) rs116519313
NM_001143780.3(SLC25A39):c.584C>T (p.Ser195Leu) rs369251462
NM_004995.4(MMP14):c.40C>T (p.Pro14Ser) rs750574703
NM_005609.4(PYGM):c.517G>A (p.Gly173Arg) rs141265458
NM_006789.4(APOBEC2):c.646G>A (p.Glu216Lys) rs150558136
NM_007118.4(TRIO):c.2776G>A (p.Gly926Arg) rs2532672263
NM_014976.2(PDCD11):c.1819C>T (p.Leu607Phe) rs765544212
NM_016148.5(SHANK1):c.2206C>T (p.Arg736Ter) rs866837836
NM_021956.5(GRIK2):c.1841T>A (p.Phe614Tyr) rs1789772602
NM_022552.5(DNMT3A):c.2645G>A (p.Arg882His) rs147001633
NM_181785.4(SLC46A3):c.731G>A (p.Arg244Gln) rs137991124

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