ClinVar Miner

Variants from Laboratory of Genetic Epidemiology, Research Centre for Medical Genetics with conflicting interpretations

Location: Russian Federation  Primary collection method: clinical testing
Minimum review status of the submission from Laboratory of Genetic Epidemiology, Research Centre for Medical Genetics: Collection method of the submission from Laboratory of Genetic Epidemiology, Research Centre for Medical Genetics:
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
95 30 0 24 1 0 15 38

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
Laboratory of Genetic Epidemiology, Research Centre for Medical Genetics pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 11 0 0 0
likely pathogenic 13 0 6 0 1
uncertain significance 6 7 0 1 0

Submitter to submitter summary #

Total submitters: 33
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
Fulgent Genetics, Fulgent Genetics 0 16 0 11 0 0 7 18
Genome-Nilou Lab 0 5 0 0 1 0 5 6
Illumina Laboratory Services, Illumina 0 6 0 2 0 0 4 6
Department of Pathology and Laboratory Medicine, Sinai Health System 0 6 0 2 0 0 3 5
3billion 0 4 0 0 0 0 4 4
Juno Genomics, Hangzhou Juno Genomics, Inc 0 2 0 1 0 0 3 4
OMIM 0 8 0 3 0 0 1 4
First Genomix Gene Laboratory, Genetic Diagnostics Department 0 2 0 1 0 0 2 3
Pele Pequeno Principe Research Institute, Faculdades Pequeno Principe 0 1 0 2 0 0 1 3
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard 0 4 0 2 0 0 0 2
Centre for Human Genetics, University of Kinshasa 0 0 0 0 0 0 2 2
Hadassah Hebrew University Medical Center 0 1 0 0 0 0 2 2
Laboratory of Medical Genetics, National & Kapodistrian University of Athens 0 1 0 2 0 0 0 2
MGZ Medical Genetics Center 0 1 0 0 0 0 2 2
Otogenetics 0 0 0 1 0 0 1 2
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 0 1 0 0 0 0 2 2
Baylor Genetics 0 7 0 1 0 0 0 1
Baylor-Hopkins Center for Mendelian Genomics, Johns Hopkins University School of Medicine 0 0 0 0 0 0 1 1
Clinical Genetics Laboratory, University Hospital Schleswig-Holstein 0 0 0 1 0 0 0 1
Department of Human Genetics, Hannover Medical School 0 1 0 0 0 0 1 1
Genetic Services Laboratory, University of Chicago 0 0 0 0 0 0 1 1
Genomic Research Center, Shahid Beheshti University of Medical Sciences 0 0 0 0 0 0 1 1
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology 0 0 0 1 0 0 0 1
Institute of Human Genetics, Heidelberg University 0 0 0 1 0 0 0 1
Institute of Human Genetics, University of Leipzig Medical Center 0 3 0 0 0 0 1 1
Mendelics 0 0 0 0 0 0 1 1
NIHR Bioresource Rare Diseases, University of Cambridge 0 1 0 1 0 0 0 1
Natera, Inc. 0 4 0 1 0 0 0 1
Neuberg Centre For Genomic Medicine, NCGM 0 0 0 1 0 0 0 1
New York Genome Center 0 0 0 1 0 0 0 1
Oxford Medical Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust 0 0 0 1 0 0 0 1
Revvity Omics, Revvity 0 3 0 1 0 0 0 1
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 1 0 0 0 0 1 1

All variants with conflicting interpretations #

Total variants: 38
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000275.3(OCA2):c.1441G>A (p.Ala481Thr) rs74653330 0.00674
NM_000372.5(TYR):c.1217C>T (p.Pro406Leu) rs104894313 0.00375
NM_000372.5(TYR):c.650G>A (p.Arg217Gln) rs61754365 0.00143
NM_000372.5(TYR):c.1037-7T>A rs61754381 0.00051
NM_000275.3(OCA2):c.1336A>G (p.Met446Val) rs140566426 0.00042
NM_000275.3(OCA2):c.593C>T (p.Pro198Leu) rs183487020 0.00035
NM_000372.5(TYR):c.140G>A (p.Gly47Asp) rs61753180 0.00030
NM_000275.3(OCA2):c.1025A>G (p.Tyr342Cys) rs142931246 0.00025
NM_000275.3(OCA2):c.1211C>T (p.Thr404Met) rs144812594 0.00023
NM_000275.3(OCA2):c.1320G>C (p.Leu440Phe) rs1800408 0.00023
NM_000275.3(OCA2):c.727C>T (p.Arg243Cys) rs138065338 0.00018
NM_016180.5(SLC45A2):c.606G>C (p.Trp202Cys) rs146802593 0.00016
NM_000372.5(TYR):c.1336G>A (p.Gly446Ser) rs104894317 0.00011
NM_016180.5(SLC45A2):c.264del (p.Gly89fs) rs775387808 0.00011
NM_000275.3(OCA2):c.2245-6C>A rs368772032 0.00009
NM_000372.5(TYR):c.325G>A (p.Gly109Arg) rs61753253 0.00009
NM_000275.3(OCA2):c.2037G>C (p.Trp679Cys) rs121918169 0.00007
NM_000275.3(OCA2):c.2080G>A (p.Ala694Thr) rs745803719 0.00005
NM_000275.3(OCA2):c.2360C>T (p.Ala787Val) rs200457227 0.00004
NM_022081.6(HPS4):c.649C>T (p.Arg217Ter) rs119471023 0.00004
NM_000372.5(TYR):c.1064C>T (p.Ala355Val) rs151206295 0.00003
NM_000372.5(TYR):c.1036+1G>A rs763715899 0.00001
NM_000372.5(TYR):c.1200G>T (p.Trp400Cys) rs145610977 0.00001
NM_000372.5(TYR):c.1255G>A (p.Gly419Arg) rs61754392 0.00001
NM_000550.3(TYRP1):c.1133A>G (p.Asn378Ser) rs771055145 0.00001
NM_016180.5(SLC45A2):c.1247G>A (p.Gly416Glu) rs773980173 0.00001
NM_000195.5(HPS1):c.1189del (p.Gln397fs) rs281865084
NM_000195.5(HPS1):c.1513C>T (p.Gln505Ter) rs769446880
NM_000195.5(HPS1):c.399-2A>G rs2538968247
NM_000195.5(HPS1):c.938-1G>A
NM_000195.5(HPS1):c.962del (p.Gly321fs) rs281865081
NM_000195.5(HPS1):c.972dup (p.Met325fs) rs281865082
NM_000372.5(TYR):c.895C>T (p.Arg299Cys) rs61754374
NM_000372.5(TYR):c.98A>C (p.Lys33Thr) rs1451372078
NM_000372.5(TYR):c.996G>A (p.Met332Ile) rs2135253415
NM_001372066.1(TFAP2A):c.769A>G (p.Arg257Gly) rs121909574
NM_016180.5(SLC45A2):c.1435del (p.Leu479fs) rs2478762696
NM_016180.5(SLC45A2):c.1519G>C (p.Val507Leu) rs3733808

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