ClinVar Miner

Variants from Genomics and Molecular Medicine Service, East Genomic Laboratory Hub, NHS Genomic Medicine Service with conflicting interpretations

Location: United Kingdom  Primary collection method: clinical testing
Minimum review status of the submission from Genomics and Molecular Medicine Service, East Genomic Laboratory Hub, NHS Genomic Medicine Service: Collection method of the submission from Genomics and Molecular Medicine Service, East Genomic Laboratory Hub, NHS Genomic Medicine Service:
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
44 97 2 34 45 0 10 82

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
Genomics and Molecular Medicine Service, East Genomic Laboratory Hub, NHS Genomic Medicine Service pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 2 7 4 0 0
likely pathogenic 13 0 2 0 0
uncertain significance 2 4 0 23 5
likely benign 0 0 15 0 4
benign 0 0 6 10 0

Submitter to submitter summary #

Total submitters: 50
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
GeneDx 0 105 0 21 16 0 3 40
Quest Diagnostics Nichols Institute San Juan Capistrano 0 79 0 19 16 0 3 38
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 36 0 5 13 0 0 18
Labcorp Genetics (formerly Invitae), Labcorp 0 40 0 2 13 0 0 15
PreventionGenetics, part of Exact Sciences 0 36 0 7 7 0 1 15
CeGaT Center for Human Genetics Tuebingen 0 37 0 8 4 0 1 13
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital 0 44 0 3 6 0 1 10
Genetic Services Laboratory, University of Chicago 0 12 0 4 5 0 1 10
Mayo Clinic Laboratories, Mayo Clinic 0 42 0 4 4 0 2 10
CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario 0 26 0 5 2 0 2 9
Revvity Omics, Revvity 0 36 0 4 3 0 2 9
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 0 39 0 4 4 0 0 8
Department of Pathology and Laboratory Medicine, Sinai Health System 0 9 0 2 2 0 3 7
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden 0 16 0 3 2 0 1 6
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 14 0 2 2 0 1 5
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ 0 21 0 2 2 0 0 4
OMIM 0 1 2 1 0 0 1 4
CZECANCA consortium 0 10 0 3 0 0 0 3
Clinical Genetics Laboratory, Skane University Hospital Lund 0 21 0 3 0 0 0 3
Dasa 0 9 0 2 0 0 1 3
Eurofins Ntd Llc (ga) 0 9 0 2 0 0 1 3
Fulgent Genetics, Fulgent Genetics 0 2 0 3 0 0 0 3
Genome Diagnostics Laboratory, Amsterdam University Medical Center 0 4 0 2 0 0 1 3
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen 0 19 0 2 0 0 1 3
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 1 0 0 2 0 1 3
Mendelics 0 3 0 0 3 0 0 3
NHS Central & South Genomic Laboratory Hub 0 5 0 3 0 0 0 3
University of Washington Department of Laboratory Medicine, University of Washington 0 1 0 1 1 0 1 3
Counsyl 0 2 0 2 0 0 0 2
Genetics Laboratory, Great Ormond Street Hospital NHS Foundation Trust, North Thames Genomic Laboratory Hub 0 21 0 2 0 0 0 2
Genome Diagnostics Laboratory, University Medical Center Utrecht 0 3 0 1 1 0 0 2
AiLife Diagnostics, AiLife Diagnostics 0 5 0 0 0 0 1 1
Cambridge Genomics Laboratory, East Genomic Laboratory Hub, NHS Genomic Medicine Service 0 26 0 1 0 0 0 1
Center of Medical Genetics and Primary Health Care 0 0 0 0 1 0 0 1
Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute 0 10 0 1 0 0 0 1
Clinical Genetics and Genomics, Karolinska University Hospital 0 16 0 1 0 0 0 1
Clinical Genetics, Academic Medical Center 0 5 0 0 1 0 0 1
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 9 0 1 0 0 0 1
Endocrine oncology group, Uppsala University 0 0 0 1 0 0 0 1
Foulkes Cancer Genetics LDI, Lady Davis Institute for Medical Research 0 10 0 0 1 0 0 1
GeneKor MSA 0 3 0 1 0 0 0 1
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center 0 2 0 1 0 0 0 1
Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine 0 0 0 1 0 0 0 1
Illumina Laboratory Services, Illumina 0 4 0 1 0 0 0 1
Institute of Human Genetics, FAU Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg 0 4 0 1 0 0 0 1
Juno Genomics, Hangzhou Juno Genomics, Inc 0 1 0 1 0 0 0 1
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) 0 9 0 0 0 0 1 1
Laboratory of Genetics, Children's Clinical University Hospital Latvia 0 7 0 1 0 0 0 1
Leiden Open Variation Database 0 3 0 0 1 0 0 1
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego 0 4 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 82
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_001048174.2(MUTYH):c.1103G>A (p.Gly368Asp) rs36053993 0.00341
NM_002528.7(NTHL1):c.503T>C (p.Ile168Thr) rs1805378 0.00155
NM_002528.7(NTHL1):c.244C>T (p.Gln82Ter) rs150766139 0.00138
NM_000179.3(MSH6):c.663A>C (p.Glu221Asp) rs41557217 0.00063
NM_002691.4(POLD1):c.883G>A (p.Val295Met) rs199545019 0.00056
NM_000038.6(APC):c.295C>T (p.Arg99Trp) rs139196838 0.00048
NM_032043.3(BRIP1):c.1255C>T (p.Arg419Trp) rs150624408 0.00030
NM_007194.4(CHEK2):c.1283C>T (p.Ser428Phe) rs137853011 0.00026
NM_024675.4(PALB2):c.1000T>G (p.Tyr334Asp) rs202241382 0.00023
NM_000059.4(BRCA2):c.7712A>G (p.Glu2571Gly) rs55689095 0.00018
NM_000535.7(PMS2):c.137G>T (p.Ser46Ile) rs121434629 0.00018
NM_000059.4(BRCA2):c.5414A>G (p.Asn1805Ser) rs80358765 0.00013
NM_000179.3(MSH6):c.3203G>A (p.Arg1068Gln) rs398123230 0.00012
NM_000251.3(MSH2):c.2203A>G (p.Ile735Val) rs2229061 0.00011
NM_000179.3(MSH6):c.3788G>A (p.Arg1263His) rs147852216 0.00010
NM_000179.3(MSH6):c.3727A>T (p.Thr1243Ser) rs147453999 0.00009
NM_007194.4(CHEK2):c.349A>G (p.Arg117Gly) rs28909982 0.00009
NM_007194.4(CHEK2):c.444+1G>A rs121908698 0.00009
NM_007294.4(BRCA1):c.314A>G (p.Tyr105Cys) rs28897673 0.00009
NM_000059.4(BRCA2):c.517-4C>G rs81002804 0.00008
NM_000179.3(MSH6):c.2281A>G (p.Arg761Gly) rs199876321 0.00008
NM_000059.4(BRCA2):c.6935A>T (p.Asp2312Val) rs80358916 0.00007
NM_000051.4(ATM):c.7271T>G (p.Val2424Gly) rs28904921 0.00006
NM_000059.4(BRCA2):c.8092G>A (p.Ala2698Thr) rs80359052 0.00005
NM_000059.4(BRCA2):c.9302T>G (p.Leu3101Arg) rs28897758 0.00005
NM_000249.4(MLH1):c.1628A>G (p.His543Arg) rs730881742 0.00004
NM_000535.7(PMS2):c.1501G>A (p.Val501Met) rs540287433 0.00004
NM_006231.4(POLE):c.1357C>G (p.Gln453Glu) rs781360770 0.00004
NM_007294.4(BRCA1):c.-16A>G rs777262055 0.00004
NM_007294.4(BRCA1):c.661G>T (p.Ala221Ser) rs80357088 0.00004
NM_058216.3(RAD51C):c.577C>T (p.Arg193Ter) rs200293302 0.00004
NM_000059.4(BRCA2):c.7565C>T (p.Ser2522Phe) rs80358985 0.00003
NM_000059.4(BRCA2):c.9271G>A (p.Val3091Ile) rs80359194 0.00003
NM_000179.3(MSH6):c.3787C>T (p.Arg1263Cys) rs367912290 0.00003
NM_002878.4(RAD51D):c.556C>T (p.Arg186Ter) rs387906843 0.00003
NM_002878.4(RAD51D):c.694C>T (p.Arg232Ter) rs587780104 0.00003
NM_007194.4(CHEK2):c.917G>C (p.Gly306Ala) rs587780192 0.00003
NM_007294.4(BRCA1):c.612G>C (p.Leu204Phe) rs80357394 0.00003
NM_032043.3(BRIP1):c.2804T>G (p.Val935Gly) rs4988356 0.00003
NM_000059.4(BRCA2):c.3299A>T (p.Asn1100Ile) rs80358575 0.00002
NM_000059.4(BRCA2):c.5896C>T (p.His1966Tyr) rs80358822 0.00002
NM_000179.3(MSH6):c.3226C>T (p.Arg1076Cys) rs63750617 0.00002
NM_002878.4(RAD51D):c.363del (p.Ala122fs) rs730881935 0.00002
NM_006231.4(POLE):c.1360-14C>T rs757413516 0.00002
NM_007294.4(BRCA1):c.2525A>G (p.Glu842Gly) rs28897684 0.00002
NM_000059.4(BRCA2):c.2698A>G (p.Asn900Asp) rs55736268 0.00001
NM_000059.4(BRCA2):c.3340C>T (p.Leu1114Phe) rs1468014859 0.00001
NM_000059.4(BRCA2):c.3628G>A (p.Asp1210Asn) rs774392592 0.00001
NM_000059.4(BRCA2):c.6271A>C (p.Ser2091Arg) rs398122550 0.00001
NM_000059.4(BRCA2):c.8952A>G (p.Ser2984=) rs876660709 0.00001
NM_000059.4(BRCA2):c.9649-9T>G rs765352313 0.00001
NM_000251.3(MSH2):c.1397A>G (p.His466Arg) rs544265737 0.00001
NM_000251.3(MSH2):c.1882G>A (p.Gly628Arg) rs371776176 0.00001
NM_004329.3(BMPR1A):c.676-3A>C rs587782760 0.00001
NM_007294.4(BRCA1):c.53T>C (p.Met18Thr) rs80356929 0.00001
NM_007294.4(BRCA1):c.5402G>A (p.Gly1801Asp) rs531210457 0.00001
NM_007294.4(BRCA1):c.755G>A (p.Arg252His) rs80357138 0.00001
NM_058216.3(RAD51C):c.571+4A>G rs587780257 0.00001
NM_058216.3(RAD51C):c.97C>T (p.Gln33Ter) rs587782528 0.00001
NM_000038.6(APC):c.677del (p.Lys226fs) rs863225371
NM_000059.4(BRCA2):c.2629C>G (p.Pro877Ala) rs80358524
NM_000059.4(BRCA2):c.467A>C (p.Asp156Ala) rs68071147
NM_000059.4(BRCA2):c.767C>T (p.Thr256Ile) rs1064794265
NM_000059.4(BRCA2):c.9104A>C (p.Tyr3035Ser) rs80359165
NM_000179.3(MSH6):c.2392C>G (p.Leu798Val) rs587779238
NM_000179.3(MSH6):c.3268_3274del (p.Glu1090fs) rs587779259
NM_000179.3(MSH6):c.3439-1G>T rs587779263
NM_000179.3(MSH6):c.3469G>A (p.Gly1157Ser) rs587779264
NM_000251.3(MSH2):c.103C>G (p.Arg35Gly) rs1060502034
NM_000251.3(MSH2):c.1147C>T (p.Arg383Ter) rs63749849
NM_000251.3(MSH2):c.1760-1G>A rs587779110
NM_000251.3(MSH2):c.1A>C (p.Met1Leu) rs267607911
NM_007194.4(CHEK2):c.58C>T (p.Gln20Ter) rs536907995
NM_007194.4(CHEK2):c.591del (p.Val198fs) rs587782245
NM_007294.4(BRCA1):c.2083G>T (p.Asp695Tyr) rs28897681
NM_007294.4(BRCA1):c.2668G>A (p.Gly890Arg) rs80357200
NM_007294.4(BRCA1):c.4357+6T>C rs80358143
NM_007294.4(BRCA1):c.5266dup (p.Gln1756fs) rs80357906
NM_007294.4(BRCA1):c.5572A>C (p.Ile1858Leu) rs765656957
NM_032043.3(BRIP1):c.2010dup (p.Glu671Ter) rs775537066
NM_058216.3(RAD51C):c.1026+5_1026+7del rs587781410
NM_058216.3(RAD51C):c.93del (p.Phe32fs) rs730881942

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