ClinVar Miner

Variants from Department of Molecular Diagnostics, Institute of Oncology Ljubljana with conflicting interpretations

Location: Slovenia — Primary collection method: clinical testing
Minimum review status of the submission from Department of Molecular Diagnostics, Institute of Oncology Ljubljana: Collection method of the submission from Department of Molecular Diagnostics, Institute of Oncology Ljubljana:
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
159 72 1 25 0 2 9 33

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 Molecular Diagnostics, Institute of Oncology Ljubljana pathogenic likely pathogenic uncertain significance association risk factor
pathogenic 1 14 5 1 2
likely pathogenic 11 0 3 0 0
uncertain significance 0 1 0 0 0

Submitter to submitter summary #

Total submitters: 22
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
Counsyl 0 30 0 10 0 0 0 10
Invitae 0 29 0 5 0 1 4 10
Mendelics 0 14 0 3 0 0 1 4
Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine 0 12 0 2 0 1 0 3
Breast Cancer Information Core (BIC) (BRCA1) 0 28 0 1 0 0 2 3
OMIM 0 15 0 1 0 1 0 2
Color Health, Inc 0 1 0 2 0 0 0 2
Institute of Human Genetics, University of Leipzig Medical Center 0 11 0 1 0 0 1 2
Ambry Genetics 0 1 0 1 0 0 0 1
King Laboratory,University of Washington 0 0 0 1 0 0 0 1
Integrated Genetics/Laboratory Corporation of America 0 10 0 1 0 0 0 1
GeneReviews 0 4 1 0 0 0 0 1
Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) 0 34 0 1 0 0 0 1
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology 0 11 0 1 0 0 0 1
Medical Genetics, University of Parma 0 1 0 1 0 0 0 1
Cancer Genetics Laboratory,Peter MacCallum Cancer Centre 0 1 0 1 0 0 0 1
Centre for Mendelian Genomics,University Medical Centre Ljubljana 0 6 0 1 0 0 0 1
Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), c/o University of Cambridge 0 31 0 1 0 0 0 1
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne 0 0 0 0 0 0 1 1
Department of Pathology and Laboratory Medicine,Sinai Health System 0 4 0 0 0 0 1 1
Cancer Diagnostics Division,Gene Solutions 0 0 0 1 0 0 0 1
Johns Hopkins Genomics, Johns Hopkins University 0 0 0 0 0 0 1 1

All variants with conflicting interpretations #

Total variants: 33
Download table as spreadsheet
HGVS dbSNP
NM_000038.6(APC):c.3920T>A (p.Ile1307Lys) rs1801155
NM_000038.6(APC):c.3927_3931del (p.Glu1309fs) rs121913224
NM_000038.6(APC):c.531+1G>A
NM_000051.3(ATM):c.8147T>C (p.Val2716Ala) rs587782652
NM_000051.3(ATM):c.8425C>T (p.Gln2809Ter) rs1555137973
NM_000051.4(ATM):c.6095G>A (p.Arg2032Lys) rs139770721
NM_000077.4(CDKN2A):c.71G>C (p.Arg24Pro) rs104894097
NM_000143.3(FH):c.214A>C (p.Thr72Pro) rs886039362
NM_000267.3(NF1):c.122A>T (p.Glu41Val)
NM_000267.3(NF1):c.6858+1G>A rs1060500355
NM_001048174.2(MUTYH):c.1435-2A>T
NM_001048174.2(MUTYH):c.241C>T (p.Arg81Trp) rs765123255
NM_001048174.2(MUTYH):c.452A>G (p.Tyr151Cys) rs34612342
NM_002485.5(NBN):c.657_661del (p.Lys219fs) rs587776650
NM_004360.5(CDH1):c.832+1G>A rs878854697
NM_006767.4(LZTR1):c.2062C>T (p.Arg688Cys) rs587777178
NM_007194.4(CHEK2):c.1100del (p.Thr367fs) rs555607708
NM_007194.4(CHEK2):c.1283C>T (p.Ser428Phe) rs137853011
NM_007194.4(CHEK2):c.1427C>T (p.Thr476Met) rs142763740
NM_007194.4(CHEK2):c.319+1G>A rs765080766
NM_007194.4(CHEK2):c.444+1G>A rs121908698
NM_007194.4(CHEK2):c.85C>T (p.Gln29Ter) rs761494650
NM_007294.4(BRCA1):c.116G>A (p.Cys39Tyr) rs80357498
NM_007294.4(BRCA1):c.191G>A (p.Cys64Tyr) rs55851803
NM_007294.4(BRCA1):c.3756_3759del (p.Ser1253fs) rs80357868
NM_007294.4(BRCA1):c.4065_4068del (p.Asn1355fs) rs80357508
NM_007294.4(BRCA1):c.4986+3G>C rs80358023
NM_007294.4(BRCA1):c.5509T>C (p.Trp1837Arg) rs80356959
NM_012222.2(MUTYH):c.725G>A (p.Arg242His) rs140342925
NM_024675.3(PALB2):c.2192T>G (p.Leu731Ter) rs1567217898
NM_024675.3(PALB2):c.3549C>G (p.Tyr1183Ter) rs118203998
NM_024675.3(PALB2):c.48G>A (p.Lys16=) rs587776405
NM_024675.4(PALB2):c.172_175del (p.Gln60fs) rs180177143

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