Variants from Foulkes Cancer Genetics LDI, Lady Davis Institute for Medical Research with conflicting interpretations

Minimum review status of the submission from Foulkes Cancer Genetics LDI, Lady Davis Institute for Medical Research:		Collection method of the submission from Foulkes Cancer Genetics LDI, Lady Davis Institute for Medical Research:
Minimum review status of the other submission:		Collection method of the other submission:
Minimum conflict level: Report conflict between different conditions
Show significances as they were submitted (without aggregation into standard terms)
		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
203	206	4	47	57	1	26	122

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
Foulkes Cancer Genetics LDI, Lady Davis Institute for Medical Research		pathogenic	likely pathogenic	uncertain significance	likely benign	benign	risk factor
	pathogenic	0	8	13	1	1	1
	likely pathogenic	8	0	5	1	1	0
	uncertain significance	3	4	3	33	25	0
	likely benign	0	0	17	0	15	0
	benign	0	0	5	16	1	0

Submitter to submitter summary #

Total submitters: 46

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	112	0	14	38	0	8	59
PreventionGenetics, part of Exact Sciences	0	44	0	8	22	0	3	33
Quest Diagnostics Nichols Institute San Juan Capistrano	0	89	0	11	18	0	2	31
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	0	49	0	8	16	0	5	29
CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario	0	43	0	11	15	0	2	28
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	0	20	0	3	22	0	2	27
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	0	41	0	6	15	0	5	26
CeGaT Center for Human Genetics Tuebingen	0	38	0	7	16	0	3	26
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	0	24	0	7	14	0	4	25
Genetic Services Laboratory, University of Chicago	0	15	0	6	13	0	1	20
Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute	0	26	0	5	12	0	1	18
Mayo Clinic Laboratories, Mayo Clinic	0	28	0	7	6	0	2	15
Department of Pathology and Laboratory Medicine, Sinai Health System	0	27	0	0	5	0	9	14
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	0	14	0	5	7	0	1	13
Biesecker Lab/Clinical Genomics Section, National Institutes of Health	0	0	4	1	4	0	1	10
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	0	14	0	2	7	0	1	10
Labcorp Genetics (formerly Invitae), Labcorp	0	62	0	3	0	0	6	9
Eurofins Ntd Llc (ga)	0	17	0	2	5	0	2	9
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	0	10	0	3	3	0	2	8
Research Molecular Genetics Laboratory, Women's College Hospital, University of Toronto	0	3	0	2	3	0	3	8
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	0	13	0	0	6	0	1	7
Genome Diagnostics Laboratory, University Medical Center Utrecht	0	7	0	2	4	0	0	6
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	0	6	0	1	2	0	3	6
Revvity Omics, Revvity	0	43	0	2	1	0	2	5
Fulgent Genetics, Fulgent Genetics	0	14	0	2	2	0	0	4
International Pleuropulmonary Blastoma Registry, Children's Hospitals and Clinics of Minnesota	0	74	0	4	0	0	0	4
ClinGen DICER1 and miRNA-Processing Gene Variant Curation Expert Panel, ClinGen	0	14	0	1	0	0	3	4
Breakthrough Genomics, Breakthrough Genomics	0	4	0	1	1	0	2	4
GeneKor MSA	0	12	0	1	1	0	1	3
Cancer Genetics and Genomics Laboratory, British Columbia Cancer Agency	0	0	0	1	2	0	0	3
Clinical Genetics Laboratory, Skane University Hospital Lund	0	23	0	1	0	0	2	3
Breast Cancer Information Core (BIC) (BRCA1)	0	0	0	0	2	0	0	2
Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA)	0	0	0	2	0	0	0	2
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	0	1	0	1	1	0	0	2
Department of Pathology and Molecular Medicine, Queen's University	0	2	0	1	1	0	0	2
OMIM	0	0	0	0	0	1	0	1
Michigan Medical Genetics Laboratories, University of Michigan	0	0	0	1	0	0	0	1
Counsyl	0	1	0	1	0	0	0	1
Mendelics	0	2	0	0	1	0	0	1
Sharing Clinical Reports Project (SCRP)	0	1	0	1	0	0	0	1
Foulkes Cancer Genetics LDI, Lady Davis Institute for Medical Research	530	0	0	0	1	0	0	1
Breast Cancer Information Core (BIC) (BRCA2)	0	1	0	0	1	0	0	1
Clinical Genetics and Genomics, Karolinska University Hospital	0	19	0	0	0	0	1	1
AiLife Diagnostics, AiLife Diagnostics	0	2	0	1	0	0	0	1
KCCC/NGS Laboratory, Kuwait Cancer Control Center	0	0	0	1	0	0	0	1
Department of Clinical Pathology, School of Medicine, Fujita Health University	0	0	0	0	1	0	0	1

All variants with conflicting interpretations #

Total variants: 122

Download table as spreadsheet

HGVS	dbSNP	gnomAD frequency
NM_177438.3(DICER1):c.1907+105C>T	rs2275182	0.22841
NM_177438.3(DICER1):c.2997T>G (p.Leu999=)	rs12018992	0.01764
NM_007294.4(BRCA1):c.2458A>G (p.Lys820Glu)	rs56082113	0.00964
NM_000059.4(BRCA2):c.5704G>A	rs4987048	0.00655
NM_000059.4(BRCA2):c.4258G>T (p.Asp1420Tyr)	rs28897727	0.00609
NM_000059.4(BRCA2):c.9976A>T (p.Lys3326Ter)	rs11571833	0.00597
NM_000059.4(BRCA2):c.5640T>G (p.Asn1880Lys)	rs11571657	0.00288
NM_000059.4(BRCA2):c.6220C>A (p.His2074Asn)	rs34309943	0.00264
NM_177438.3(DICER1):c.1377-4T>G	rs192490028	0.00240
NM_177438.3(DICER1):c.485G>A (p.Gly162Asp)	rs142815547	0.00218
NM_007294.4(BRCA1):c.2167A>G (p.Asn723Asp)	rs4986845	0.00209
NM_000059.4(BRCA2):c.7150C>A (p.Gln2384Lys)	rs55977008	0.00203
NM_000059.4(BRCA2):c.8503T>C (p.Ser2835Pro)	rs11571746	0.00202
NM_177438.3(DICER1):c.20A>G (p.Gln7Arg)	rs117358479	0.00165
NM_000059.4(BRCA2):c.8567A>C (p.Glu2856Ala)	rs11571747	0.00158
NM_007294.4(BRCA1):c.2109A>G (p.Thr703=)	rs4986844	0.00147
NM_000059.4(BRCA2):c.8149G>T (p.Ala2717Ser)	rs28897747	0.00127
NM_000059.4(BRCA2):c.6821G>T (p.Gly2274Val)	rs55712212	0.00126
NM_177438.3(DICER1):c.5145C>T (p.Leu1715=)	rs139500905	0.00121
NM_007294.4(BRCA1):c.591C>T (p.Cys197=)	rs1799965	0.00117
NM_177438.3(DICER1):c.4014G>A (p.Ala1338=)	rs143454689	0.00099
NM_007294.4(BRCA1):c.-86C>T	rs143160357	0.00077
NM_000059.4(BRCA2):c.1151C>T (p.Ser384Phe)	rs41293475	0.00074
NM_007294.4(BRCA1):c.5348T>C (p.Met1783Thr)	rs55808233	0.00058
NM_000059.4(BRCA2):c.1964C>G (p.Pro655Arg)	rs28897712	0.00054
NM_000059.4(BRCA2):c.8187G>T (p.Lys2729Asn)	rs80359065	0.00032
NM_007294.4(BRCA1):c.2368A>G (p.Thr790Ala)	rs41286298	0.00029
NM_007294.4(BRCA1):c.736T>G (p.Leu246Val)	rs28897675	0.00026
NM_177438.3(DICER1):c.1124C>G (p.Pro375Arg)	rs148758903	0.00025
NM_007294.4(BRCA1):c.1486C>T (p.Arg496Cys)	rs28897676	0.00023
NM_000059.4(BRCA2):c.6322C>T (p.Arg2108Cys)	rs55794205	0.00019
NM_007294.4(BRCA1):c.3748G>A (p.Glu1250Lys)	rs28897686	0.00017
NM_007294.4(BRCA1):c.4132G>A (p.Val1378Ile)	rs28897690	0.00017
NM_177438.3(DICER1):c.4616C>T (p.Thr1539Met)	rs747901058	0.00013
NM_000059.4(BRCA2):c.1889C>T (p.Thr630Ile)	rs80358479	0.00012
NM_007294.4(BRCA1):c.1065G>A (p.Lys355=)	rs41286292	0.00011
NM_007294.4(BRCA1):c.2002C>T (p.Leu668Phe)	rs80357250	0.00011
NM_007294.4(BRCA1):c.2596C>T (p.Arg866Cys)	rs41286300	0.00011
NM_000059.4(BRCA2):c.9501+3A>T	rs61757642	0.00008
NM_000059.4(BRCA2):c.2957A>G (p.Asn986Ser)	rs28897718	0.00006
NM_000059.4(BRCA2):c.7057G>C (p.Gly2353Arg)	rs80358935	0.00006
NM_007294.4(BRCA1):c.4636G>A (p.Asp1546Asn)	rs28897691	0.00006
NM_000059.4(BRCA2):c.4570T>G (p.Phe1524Val)	rs56386506	0.00004
NM_000059.4(BRCA2):c.9586A>G (p.Lys3196Glu)	rs80359228	0.00004
NM_000059.4(BRCA2):c.3225T>C (p.Ser1075=)	rs779228375	0.00003
NM_000059.4(BRCA2):c.3581G>A (p.Gly1194Asp)	rs28897721	0.00003
NM_000059.4(BRCA2):c.4670C>G (p.Thr1557Ser)	rs80358698	0.00003
NM_000059.4(BRCA2):c.5634C>G (p.Asn1878Lys)	rs80358784	0.00003
NM_000059.4(BRCA2):c.6275_6276del (p.Leu2092fs)	rs11571658	0.00003
NM_000059.4(BRCA2):c.8010G>A (p.Ser2670=)	rs146430937	0.00003
NM_177438.3(DICER1):c.4740G>T (p.Gln1580His)	rs369465519	0.00003
NM_000059.4(BRCA2):c.5645C>A (p.Ser1882Ter)	rs80358785	0.00002
NM_000059.4(BRCA2):c.6017G>C (p.Ser2006Thr)	rs144784912	0.00002
NM_000059.4(BRCA2):c.7021C>T (p.Arg2341Cys)	rs41293505	0.00002
NM_000059.4(BRCA2):c.708T>C (p.His236=)	rs185506536	0.00002
NM_000059.4(BRCA2):c.8386C>T (p.Pro2796Ser)	rs146120136	0.00002
NM_000059.4(BRCA2):c.9728C>T (p.Pro3243Leu)	rs80359241	0.00002
NM_007294.4(BRCA1):c.5074+6C>G	rs80358032	0.00002
NM_177438.3(DICER1):c.184G>A (p.Val62Ile)	rs746671039	0.00002
NM_177438.3(DICER1):c.3334A>G (p.Asn1112Asp)	rs587778229	0.00002
NM_177438.3(DICER1):c.4199A>G (p.Asp1400Gly)	rs139536688	0.00002
NM_000059.4(BRCA2):c.1244A>G (p.His415Arg)	rs80358417	0.00001
NM_000059.4(BRCA2):c.2122T>A (p.Ser708Thr)	rs80358488	0.00001
NM_000059.4(BRCA2):c.6953G>A (p.Arg2318Gln)	rs80358921	0.00001
NM_000059.4(BRCA2):c.7992T>A (p.Ile2664=)	rs80359800	0.00001
NM_007294.4(BRCA1):c.1105G>A (p.Asp369Asn)	rs56056711	0.00001
NM_007294.4(BRCA1):c.212+3A>G	rs80358083	0.00001
NM_007294.4(BRCA1):c.4096+1G>A	rs80358178	0.00001
NM_007294.4(BRCA1):c.4816A>G (p.Lys1606Glu)	rs80356943	0.00001
NM_007294.4(BRCA1):c.4986+6T>C	rs80358086	0.00001
NM_007294.4(BRCA1):c.5096G>A (p.Arg1699Gln)	rs41293459	0.00001
NM_007294.4(BRCA1):c.5506G>A (p.Glu1836Lys)	rs80356942	0.00001
NM_177438.3(DICER1):c.884C>G (p.Ser295Cys)	rs548231008	0.00001
NM_000059.4(BRCA2):c.314T>G (p.Leu105Ter)	rs80358561
NM_000059.4(BRCA2):c.316+5G>A	rs81002840
NM_000059.4(BRCA2):c.6466_6469del (p.Ser2156fs)	rs80359596
NM_000059.4(BRCA2):c.6643del (p.Tyr2215fs)	rs80359614
NM_000059.4(BRCA2):c.6938-2A>G	rs81002863
NM_000059.4(BRCA2):c.7007+5G>A	rs81002816
NM_000059.4(BRCA2):c.8084C>T (p.Ser2695Leu)	rs80359048
NM_000059.4(BRCA2):c.9004G>A (p.Glu3002Lys)	rs80359152
NM_000059.4(BRCA2):c.9104A>C (p.Tyr3035Ser)	rs80359165
NM_000059.4(BRCA2):c.956A>C (p.Asn319Thr)	rs55939572
NM_000059.4(BRCA2):c.956A>G (p.Asn319Ser)	rs55939572
NM_000059.4(BRCA2):c.9613_9614delinsCT (p.Ala3205Leu)	rs276174926
NM_000059.4(BRCA2):c.9925G>T (p.Glu3309Ter)	rs80359251
NM_007294.4(BRCA1):c.1441C>G (p.Leu481Val)	rs1397842308
NM_007294.4(BRCA1):c.2722G>T (p.Glu908Ter)	rs80356978
NM_007294.4(BRCA1):c.3113A>C (p.Glu1038Ala)	rs16941
NM_007294.4(BRCA1):c.3179A>C (p.Glu1060Ala)	rs80357184
NM_007294.4(BRCA1):c.3600G>C (p.Gln1200His)	rs56214134
NM_007294.4(BRCA1):c.3668_3671dup (p.Cys1225fs)	rs80357797
NM_007294.4(BRCA1):c.4096+3A>G	rs80358015
NM_007294.4(BRCA1):c.4399C>T (p.Gln1467Ter)	rs397509171
NM_007294.4(BRCA1):c.4654T>C (p.Tyr1552His)	rs1265352633
NM_007294.4(BRCA1):c.4675+1G>A	rs80358044
NM_007294.4(BRCA1):c.5090G>A (p.Cys1697Tyr)	rs397507241
NM_007294.4(BRCA1):c.5102_5103del (p.Leu1701fs)	rs80357608
NM_007294.4(BRCA1):c.5216A>G (p.Asp1739Gly)	rs80357227
NM_007294.4(BRCA1):c.5266dup (p.Gln1756fs)	rs80357906
NM_007294.4(BRCA1):c.548-9del	rs273902774
NM_007294.4(BRCA1):c.5521A>C (p.Ser1841Arg)	rs80357299
NM_177438.3(DICER1):c.2040+54dup	rs141723381
NM_177438.3(DICER1):c.2516C>T (p.Ser839Phe)	rs387906934
NM_177438.3(DICER1):c.2987+1G>A	rs1555370248
NM_177438.3(DICER1):c.4206+7_4206+8dup	rs1555368535
NM_177438.3(DICER1):c.4254GGA[2] (p.Glu1420del)	rs544960260
NM_177438.3(DICER1):c.4748T>G (p.Leu1583Arg)	rs137852976
NM_177438.3(DICER1):c.4806C>T (p.Ala1602=)	rs1890302137
NM_177438.3(DICER1):c.4889G>T (p.Arg1630Leu)	rs368343829
NM_177438.3(DICER1):c.5096-12G>A	rs1566750865
NM_177438.3(DICER1):c.5123G>A (p.Gly1708Glu)	rs886037724
NM_177438.3(DICER1):c.5126A>G (p.Asp1709Gly)	rs1555366979
NM_177438.3(DICER1):c.5138A>T (p.Asp1713Val)	rs1595331224
NM_177438.3(DICER1):c.5425G>A (p.Gly1809Arg)	rs1595314951
NM_177438.3(DICER1):c.5428G>T (p.Asp1810Tyr)	rs775912475
NM_177438.3(DICER1):c.5438A>C (p.Glu1813Ala)	rs1889806272
NM_177438.3(DICER1):c.5452G>A (p.Ala1818Thr)	rs1889802883
NM_177438.3(DICER1):c.5465A>T (p.Asp1822Val)	rs886037729
NM_177438.3(DICER1):c.5656G>A (p.Gly1886Arg)	rs1566744851
NM_177438.3(DICER1):c.735-1_741delinsA	rs886037731
NM_177438.3(DICER1):c.904-1G>C	rs1566803555

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