ClinVar Miner

Variants from Department of Medical Genetics, Oslo University Hospital with conflicting interpretations

Location: Norway — Primary collection method: clinical testing
Minimum review status of the submission from Department of Medical Genetics, Oslo University Hospital: Collection method of the submission from Department of Medical Genetics, Oslo University Hospital:
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
58 167 2 34 1 0 19 47

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 Medical Genetics, Oslo University Hospital pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 2 17 5 0 0
likely pathogenic 17 0 12 0 1
uncertain significance 0 1 0 1 0

Submitter to submitter summary #

Total submitters: 25
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 50 0 13 0 0 0 13
Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), c/o University of Cambridge 0 130 0 10 0 0 0 10
Breast Cancer Information Core (BIC) (BRCA1) 0 74 0 2 0 0 8 9
Sharing Clinical Reports Project (SCRP) 0 96 0 2 0 0 5 7
Breast Cancer Information Core (BIC) (BRCA2) 0 43 0 1 0 0 5 6
Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) 0 162 0 6 0 0 0 6
OMIM 0 35 0 4 0 0 0 4
GeneReviews 0 3 2 2 0 0 0 4
Department of Medical Genetics, University Hospital of North Norway 0 2 0 1 0 0 2 3
Mendelics 0 9 0 1 0 0 1 2
Database of Curated Mutations (DoCM) 0 0 0 2 0 0 0 2
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics,Children's Hospital of Philadelphia 0 7 0 1 0 0 0 1
Fulgent Genetics,Fulgent Genetics 0 4 0 1 0 0 0 1
Quest Diagnostics Nichols Institute San Juan Capistrano 0 16 0 1 0 0 0 1
ClinVar Staff, National Center for Biotechnology Information (NCBI) 0 0 0 0 0 0 1 1
Illumina Clinical Services Laboratory,Illumina 0 1 0 1 0 0 0 1
Pathway Genomics 0 7 0 0 0 0 1 1
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology 0 8 0 1 0 0 0 1
CeGaT Praxis fuer Humangenetik Tuebingen 0 0 0 0 1 0 0 1
Centre for Mendelian Genomics,University Medical Centre Ljubljana 0 0 0 0 0 0 1 1
Institute of Human Genetics, University of Leipzig Medical Center 0 12 0 0 0 0 1 1
Department of Pathology and Laboratory Medicine,Sinai Health System 0 8 0 1 0 0 0 1
Geisinger Autism and Developmental Medicine Institute,Geisinger Health System 0 1 0 1 0 0 0 1
Kariminejad - Najmabadi Pathology & Genetics Center 0 0 0 1 0 0 0 1
Cavalleri Lab, Royal College of Surgeons in Ireland 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 47
Download table as spreadsheet
HGVS dbSNP
NM_000059.3(BRCA2):c.3545_3546del (p.Gln1181_Phe1182insTer) rs80359388
NM_000059.3(BRCA2):c.4258del (p.Asp1420fs) rs80359436
NM_000059.3(BRCA2):c.631+4A>G rs397507841
NM_000059.3(BRCA2):c.7753G>A (p.Gly2585Arg) rs80359002
NM_000059.3(BRCA2):c.8177A>G (p.Tyr2726Cys) rs80359064
NM_000059.3(BRCA2):c.9253dupA (p.Thr3085Asnfs) rs80359752
NM_000059.4(BRCA2):c.1296_1297del (p.Asn433fs) rs80359276
NM_000059.4(BRCA2):c.1456C>T (p.Gln486Ter) rs80358434
NM_000059.4(BRCA2):c.145G>T (p.Glu49Ter) rs80358435
NM_000059.4(BRCA2):c.517-2A>G rs81002858
NM_000059.4(BRCA2):c.7024C>T (p.Gln2342Ter) rs80358928
NM_000059.4(BRCA2):c.7878G>C (p.Trp2626Cys) rs80359013
NM_000059.4(BRCA2):c.8229_8243del (p.Arg2744_Gly2748del) rs80359698
NM_000059.4(BRCA2):c.9154C>T (p.Arg3052Trp) rs45580035
NM_000059.4(BRCA2):c.9699_9702del rs80359775
NM_000141.5(FGFR2):c.1025G>A (p.Cys342Tyr) rs121918487
NM_000141.5(FGFR2):c.1124A>G (p.Tyr375Cys) rs121913478
NM_000141.5(FGFR2):c.755C>G (p.Ser252Trp) rs79184941
NM_000142.5(FGFR3):c.749C>G (p.Pro250Arg) rs4647924
NM_000528.4(MAN2B1):c.1055T>C (p.Leu352Pro) rs864621980
NM_000748.3(CHRNB2):c.1378C>G (p.Arg460Gly) rs202079239
NM_002180.2(IGHMBP2):c.1478C>T (p.Thr493Ile) rs780594709
NM_002180.2(IGHMBP2):c.449+1G>T rs797044802
NM_003718.5(CDK13):c.2524A>G (p.Asn842Asp) rs1554333853
NM_004429.4(EFNB1):c.161C>T (p.Pro54Leu) rs104894801
NM_006205.3(PDE6H):c.35C>G (p.Ser12Ter) rs200311463
NM_006563.4(KLF1):c.519_525dup (p.Gly176fs) rs483352838
NM_006662.3(SRCAP):c.7303C>T (p.Arg2435Ter) rs199469465
NM_007294.3(BRCA1):c.4096+3A>G rs80358015
NM_007294.4(BRCA1):c.115T>G (p.Cys39Gly) rs80357164
NM_007294.4(BRCA1):c.130T>A (p.Cys44Ser) rs80357327
NM_007294.4(BRCA1):c.140G>T (p.Cys47Phe) rs80357150
NM_007294.4(BRCA1):c.3228_3229del (p.Gly1077fs) rs80357635
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.4484G>A (p.Arg1495Lys) rs80357389
NM_007294.4(BRCA1):c.5074+2T>C rs80358089
NM_007294.4(BRCA1):c.5153G>C (p.Trp1718Ser) rs41293461
NM_007294.4(BRCA1):c.5212G>A (p.Gly1738Arg) rs80356937
NM_007294.4(BRCA1):c.5213G>A (p.Gly1738Glu) rs80357450
NM_007294.4(BRCA1):c.5309G>T (p.Gly1770Val) rs863224765
NM_007294.4(BRCA1):c.5434C>G (p.Pro1812Ala) rs1800751
NM_007294.4(BRCA1):c.5503C>T (p.Arg1835Ter) rs41293465
NM_007294.4(BRCA1):c.5513T>G (p.Val1838Gly) rs80357107
NM_007294.4(BRCA1):c.65T>C (p.Leu22Ser) rs80357438
NM_052989.3(IFT122):c.965C>T (p.Ser322Phe) rs267607192
Single allele

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