ClinVar Miner

Variants from Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University with conflicting interpretations

Location: Japan  Primary collection method: clinical testing
Minimum review status of the submission from Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University: Collection method of the submission from Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University:
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
83 77 0 32 5 0 8 44

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
Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 17 2 0 0
likely pathogenic 4 0 3 3 0
uncertain significance 0 0 0 3 2
likely benign 0 0 1 0 11

Submitter to submitter summary #

Total submitters: 17
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
Invitae 0 73 0 16 4 0 6 26
Genome-Nilou Lab 0 57 0 12 3 0 3 18
Color Diagnostics, LLC DBA Color Health 0 4 0 7 0 0 0 7
KCCC/NGS Laboratory, Kuwait Cancer Control Center 0 4 0 5 0 0 0 5
deCODE genetics, Amgen 0 0 0 3 0 0 0 3
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center 0 1 0 1 0 0 2 3
All of Us Research Program, National Institutes of Health 0 4 0 3 0 0 0 3
Center for Human Genetics, Inc, Center for Human Genetics, Inc 0 9 0 2 0 0 0 2
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 0 6 0 1 0 0 1 2
Illumina Laboratory Services, Illumina 0 7 0 2 0 0 0 2
Institute of Human Genetics, University of Leipzig Medical Center 0 2 0 2 0 0 0 2
Myriad Genetics, Inc. 0 5 0 2 0 0 0 2
Baylor Genetics 0 4 0 0 1 0 0 1
Athena Diagnostics Inc 0 12 0 1 0 0 0 1
Molecular Biology Laboratory, Fundació Puigvert 0 1 0 1 0 0 0 1
3billion 0 7 0 1 0 0 0 1
Neuberg Centre For Genomic Medicine, NCGM 0 2 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 44
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000368.5(TSC1):c.2829C>T (p.Ala943=) rs4962081 0.08329
NM_000368.5(TSC1):c.3324C>T (p.Gly1108=) rs35593170 0.00704
NM_000548.5(TSC2):c.856A>G (p.Met286Val) rs1800748 0.00083
NM_000548.5(TSC2):c.1593C>T (p.Ile531=) rs45517180 0.00051
NM_000548.5(TSC2):c.5028G>A (p.Leu1676=) rs45475501 0.00026
NM_000368.5(TSC1):c.1936A>G (p.Met646Val) rs145741748 0.00016
NM_000368.5(TSC1):c.2075G>A (p.Arg692Gln) rs199755731 0.00011
NM_000548.5(TSC2):c.4136C>T (p.Ser1379Leu) rs137854065 0.00007
NM_000368.5(TSC1):c.2696C>G (p.Thr899Ser) rs76801599 0.00005
NM_000548.5(TSC2):c.5210C>T (p.Pro1737Leu) rs749326176 0.00004
NM_000548.5(TSC2):c.1096G>A (p.Glu366Lys) rs45517148 0.00003
NM_000548.5(TSC2):c.1882C>T (p.Arg628Cys) rs45437797 0.00003
NM_000548.5(TSC2):c.2585C>T (p.Ala862Val) rs45517249 0.00003
NM_000548.5(TSC2):c.4930G>A (p.Asp1644Asn) rs137853999 0.00002
NM_000548.5(TSC2):c.993C>T (p.Asn331=) rs45517153 0.00002
NM_000548.5(TSC2):c.4137G>A (p.Ser1379=) rs769653533 0.00001
NM_000368.5(TSC1):c.1525C>T (p.Arg509Ter) rs118203542
NM_000368.5(TSC1):c.1996A>T (p.Lys666Ter) rs1845604585
NM_000368.5(TSC1):c.2626-1G>A rs397514847
NM_000368.5(TSC1):c.2806C>T (p.Gln936Ter) rs118203735
NM_000368.5(TSC1):c.3112AGC[7] (p.Ser1043dup) rs2234980
NM_000368.5(TSC1):c.363+1G>T rs118203372
NM_000368.5(TSC1):c.364-2A>G rs1846685279
NM_000368.5(TSC1):c.664-15A>G rs118203422
NM_000368.5(TSC1):c.733C>T (p.Arg245Ter) rs118203434
NM_000368.5(TSC1):c.982C>T (p.Gln328Ter) rs1554817388
NM_000548.5(TSC2):c.1096G>T (p.Glu366Ter) rs45517148
NM_000548.5(TSC2):c.1513C>T (p.Arg505Ter) rs45517179
NM_000548.5(TSC2):c.1717-1G>A rs45517192
NM_000548.5(TSC2):c.1778A>G (p.His593Arg) rs45517198
NM_000548.5(TSC2):c.1832G>A (p.Arg611Gln) rs28934872
NM_000548.5(TSC2):c.1864C>T (p.Arg622Trp) rs397514914
NM_000548.5(TSC2):c.2339T>C (p.Leu780Pro) rs2151328709
NM_000548.5(TSC2):c.2714G>A (p.Arg905Gln) rs45517259
NM_000548.5(TSC2):c.2764_2765del (p.Leu922fs) rs1555508929
NM_000548.5(TSC2):c.278G>A (p.Arg93Gln) rs1222477746
NM_000548.5(TSC2):c.3095G>C (p.Arg1032Pro) rs45491698
NM_000548.5(TSC2):c.4628A>G (p.His1543Arg) rs2090628516
NM_000548.5(TSC2):c.4909AAG[1] (p.Lys1638del) rs137854261
NM_000548.5(TSC2):c.5024C>T (p.Pro1675Leu) rs45483392
NM_000548.5(TSC2):c.5228G>A (p.Arg1743Gln) rs45507199
NM_000548.5(TSC2):c.5238_5255del (p.His1746_Arg1751del) rs137854218
NM_000548.5(TSC2):c.5422_5423del (p.Ter1808ArgextTer?) rs137854027
NM_001042492.3(NF1):c.2850+1G>T rs1131691122

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