ClinVar Miner

Variants from Daryl Scott Lab, Baylor College of Medicine with conflicting interpretations

Location: United States  Primary collection method: clinical testing
Minimum review status of the submission from Daryl Scott Lab, Baylor College of Medicine: Collection method of the submission from Daryl Scott Lab, Baylor College of Medicine:
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
270 101 0 36 12 3 21 68

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
Daryl Scott Lab, Baylor College of Medicine pathogenic likely pathogenic uncertain significance likely benign benign affects pathogenic, low penetrance protective other
pathogenic 0 31 6 2 1 1 1 1 1
likely pathogenic 5 0 4 0 0 0 0 0 0
uncertain significance 8 6 0 9 2 0 0 0 0
likely benign 1 0 2 0 0 0 0 0 0

Submitter to submitter summary #

Total submitters: 71
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
Invitae 0 28 0 2 6 1 4 13
Baylor Genetics 0 65 0 5 1 0 5 11
OMIM 0 34 0 0 0 1 5 6
Genome-Nilou Lab 0 7 0 3 2 0 1 6
Illumina Laboratory Services, Illumina 0 17 0 1 3 0 2 5
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne 0 7 0 3 0 0 2 4
Counsyl 0 3 0 2 0 0 1 3
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 12 0 3 0 0 0 3
Natera, Inc. 0 7 0 1 0 0 2 3
Centre for Mendelian Genomics, University Medical Centre Ljubljana 0 7 0 2 0 0 1 3
Undiagnosed Diseases Network, NIH 0 5 0 3 0 0 1 3
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego 0 3 0 1 0 0 2 3
Myriad Genetics, Inc. 0 5 0 3 0 0 0 3
Athena Diagnostics Inc 0 1 0 1 1 0 1 2
GeneDx 0 10 0 2 0 0 1 2
Revvity Omics, Revvity 0 23 0 1 1 0 0 2
PreventionGenetics, part of Exact Sciences 0 5 0 0 1 0 1 2
Eurofins Ntd Llc (ga) 0 5 0 2 0 1 1 2
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 0 11 0 1 0 0 1 2
CeGaT Center for Human Genetics Tuebingen 0 4 0 0 1 0 1 2
SIB Swiss Institute of Bioinformatics 0 1 0 2 0 0 0 2
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 4 0 0 0 0 1 1
Ambry Genetics 0 1 0 1 0 0 0 1
Elsea Laboratory, Baylor College of Medicine 0 1 0 0 0 0 1 1
Centre for Inherited Metabolic Diseases, Karolinska University Hospital 0 0 0 0 0 0 1 1
Institute of Human Genetics, University of Ulm 0 0 0 0 0 0 1 1
Mendelics 0 7 0 1 0 0 0 1
GeneReviews 0 14 0 0 0 0 1 1
Mayo Clinic Laboratories, Mayo Clinic 0 1 0 1 0 0 1 1
Quest Diagnostics Nichols Institute San Juan Capistrano 0 1 0 0 0 0 1 1
ClinVar Staff, National Center for Biotechnology Information (NCBI) 0 0 0 1 0 0 0 1
Department Of Translational Genomics (developmental Genetics Section), King Faisal Specialist Hospital & Research Centre 0 0 0 1 0 0 0 1
Genomic Research Center, Shahid Beheshti University of Medical Sciences 0 3 0 0 0 0 1 1
Department of Medical Genetics, Oslo University Hospital 0 0 0 1 0 0 0 1
Vavilov Institute of General Genetics RAS, Laboratory of Evolutional Genomics 0 0 0 0 0 1 0 1
Center for Individualized Medicine, Mayo Clinic 0 0 0 1 0 0 0 1
University of Washington Center for Mendelian Genomics, University of Washington 0 1 0 1 0 0 0 1
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology 0 5 0 1 0 0 0 1
Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine 0 0 0 1 0 0 1 1
Genome Sciences Centre, British Columbia Cancer Agency 0 0 0 1 0 0 0 1
Institute of Human Genetics, University Hospital of Duesseldorf 0 0 0 1 0 0 0 1
NIHR Bioresource Rare Diseases, University of Cambridge 0 1 0 1 0 0 0 1
Center for Molecular Medicine, Children’s Hospital of Fudan University 0 1 0 1 0 0 0 1
Institute of Human Genetics, University of Leipzig Medical Center 0 11 0 1 0 0 0 1
Department of Pathology and Laboratory Medicine, Sinai Health System 0 0 0 0 0 0 1 1
Laboratoire de Génétique Moléculaire, CHU Bordeaux 0 1 0 1 0 0 0 1
Geisinger Autism and Developmental Medicine Institute, Geisinger Health System 0 1 0 1 0 0 1 1
Rare Disease Group, Clinical Genetics, Karolinska Institutet 0 0 0 1 0 0 1 1
Institute of Cellular and Molecular Medicine, Copenhagen University 0 0 0 1 0 0 0 1
Leiden Open Variation Database 0 2 0 0 0 0 1 1
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) 0 0 0 0 0 0 1 1
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 4 0 0 0 0 1 1
Laboratoire de Genetique Moleculaire, Centre Hospitalier Universitaire de Bordeaux 0 0 0 0 0 0 1 1
Medical Genetics Lab, Policlinico S. Orsola.Malpighi 0 0 0 1 0 0 1 1
Medical Cytogenetics and Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano 0 1 0 0 0 0 1 1
Department Of Genetics, Sultan Qaboos University Hospital, Sultan Qaboos University 0 0 0 0 0 0 1 1
UNC Molecular Genetics Laboratory, University of North Carolina at Chapel Hill 0 1 0 1 0 0 0 1
St. Jude Molecular Pathology, St. Jude Children's Research Hospital 0 1 0 1 0 0 0 1
Genomic Medicine Lab, University of California San Francisco 0 3 0 1 0 0 0 1
Department of Pediatrics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology 0 0 0 1 0 0 0 1
Molecular Pathology Diagnostics Labratory, University of Iowa Hospitals & Clinics 0 0 0 1 0 0 0 1
Biochemistry Laboratory of CDMU, Chengde Medical University 0 0 0 1 0 0 0 1
Zotz-Klimas Genetics Lab, MVZ Zotz Klimas 0 2 0 1 0 0 0 1
Medical Genetics Laboratory, Tarbiat Modares University 0 0 0 0 0 0 1 1
Rare Disease Group, University of Exeter 0 0 0 1 0 0 0 1
New York Genome Center 0 5 0 1 0 0 1 1
Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University 0 0 0 1 0 0 0 1
Molecular Biology Laboratory, Fundació Puigvert 0 1 0 1 0 0 0 1
Precision Medical Center, Maternal and Child Health Hospital of Hubei Province 0 0 0 0 0 0 1 1
3billion 0 13 0 1 0 0 0 1
IU Genetic Testing Laboratories, Indiana University School of Medicine 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 68
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_005105.5(RBM8A):c.-21G>A rs139428292 0.01871
NM_000666.3(ACY1):c.1057C>T (p.Arg353Cys) rs121912698 0.00260
NM_004525.3(LRP2):c.5390A>G (p.Asn1797Ser) rs138070797 0.00234
NM_001363.4(DKC1):c.-142C>G rs199422241 0.00229
NM_024649.5(BBS1):c.1169T>G (p.Met390Arg) rs113624356 0.00212
NM_152743.4(BRAT1):c.1828C>T (p.Arg610Trp) rs61753094 0.00152
NM_213607.3(CCDC103):c.461A>C (p.His154Pro) rs145457535 0.00123
NM_144508.5(KNL1):c.6482A>G (p.Asp2161Gly) rs142872154 0.00097
NM_001366722.1(GRIP1):c.160G>A (p.Val54Ile) rs199768740 0.00087
NM_000388.4(CASR):c.1631G>A (p.Arg544Gln) rs115230894 0.00086
NM_016366.3(CABP2):c.590T>C (p.Ile197Thr) rs145369252 0.00068
NM_004278.4(PIGL):c.500T>C (p.Leu167Pro) rs145303331 0.00062
NM_000520.6(HEXA):c.1274_1277dup (p.Tyr427fs) rs387906309 0.00046
NM_020117.11(LARS1):c.1292T>A (p.Val431Asp) rs150429680 0.00041
NM_015335.5(MED13L):c.3214G>A (p.Val1072Ile) rs142907547 0.00035
NM_024105.4(ALG12):c.437G>A (p.Arg146Gln) rs121907932 0.00016
NM_001164508.2(NEB):c.21173C>T (p.Thr7058Ile) rs200523155 0.00015
NM_000141.5(FGFR2):c.289G>A (p.Ala97Thr) rs372430349 0.00011
NM_032043.3(BRIP1):c.2392C>T (p.Arg798Ter) rs137852986 0.00010
NM_004525.3(LRP2):c.10906C>T (p.Arg3636Trp) rs747833963 0.00009
NM_000136.3(FANCC):c.1642C>T (p.Arg548Ter) rs104886457 0.00007
NM_001018115.3(FANCD2):c.2605+1G>A rs142365855 0.00003
NM_001360.3(DHCR7):c.1342G>A (p.Glu448Lys) rs80338864 0.00003
NM_144643.4(SCLT1):c.638C>T (p.Thr213Ile) rs760824351 0.00003
NM_003235.5(TG):c.2359C>T (p.Arg787Ter) rs752966476 0.00002
NM_000540.3(RYR1):c.9472+9G>A rs1392237616 0.00001
NM_001048166.1(STIL):c.3838C>T (p.Arg1280Cys) rs199634446 0.00001
NM_001101426.4(CRPPA):c.1354T>A (p.Ter452Arg) rs186882839 0.00001
NM_001113378.2(FANCI):c.2422A>T (p.Lys808Ter) rs375656231 0.00001
NM_003482.4(KMT2D):c.14923C>T (p.Arg4975Cys) rs781012274 0.00001
NM_000314.8(PTEN):c.203A>G (p.Tyr68Cys) rs876660634
NM_000521.4(HEXB):c.1535_1536del (p.Arg512fs) rs794727091
NM_000521.4(HEXB):c.160C>A (p.Pro54Thr) rs778119481
NM_000535.7(PMS2):c.1831dup (p.Ile611fs) rs63750250
NM_001042681.2(RERE):c.1681_1684del (p.Glu561fs) rs1641706044
NM_001042681.2(RERE):c.4304A>G (p.His1435Arg) rs1553154130
NM_001083962.2(TCF4):c.1486+1G>T rs2048816852
NM_001100913.3(PACS2):c.625G>A (p.Glu209Lys) rs1555408401
NM_001101426.4(CRPPA):c.1315G>T (p.Glu439Ter) rs1202301143
NM_001127392.3(MYRF):c.2084G>A (p.Arg695His) rs1382225004
NM_001164508.2(NEB):c.24666del (p.Phe8222fs) rs794727136
NM_001197104.2(KMT2A):c.3460C>T (p.Arg1154Trp) rs1555038090
NM_001267550.2(TTN):c.66968del (p.Asn22323fs) rs2154176360
NM_001356.5(DDX3X):c.1595C>T (p.Thr532Met) rs1064795387
NM_001360.3(DHCR7):c.964-1G>C rs138659167
NM_001368894.2(PAX6):c.52G>C (p.Gly18Arg) rs886044289
NM_001429.4(EP300):c.2660C>T (p.Thr887Ile) rs953108559
NM_003072.5(SMARCA4):c.2656A>G (p.Met886Val) rs2146416371
NM_003072.5(SMARCA4):c.2936G>A (p.Arg979Gln)
NM_003482.4(KMT2D):c.1967del (p.Leu656fs) rs772870804
NM_003718.5(CDK13):c.2524A>G (p.Asn842Asp) rs1554333853
NM_003924.4(PHOX2B):c.385G>A (p.Glu129Lys) rs1560466246
NM_006009.4(TUBA1A):c.641G>A (p.Arg214His) rs1057517843
NM_006015.6(ARID1A):c.98_107del (p.Glu33fs) rs2124740134
NM_006245.4(PPP2R5D):c.598G>A (p.Glu200Lys) rs863225079
NM_006296.7(VRK2):c.*102_*105dup rs759217526
NM_013450.4(BAZ2B):c.2105dup (p.Ser703fs)
NM_014159.7(SETD2):c.5218C>T (p.Arg1740Trp) rs1057523157
NM_015338.6(ASXL1):c.1934dup (p.Gly646fs) rs750318549
NM_015506.3(MMACHC):c.382TAC[2] (p.Tyr130del) rs796051998
NM_016464.5(TMEM138):c.389A>G (p.Tyr130Cys) rs387907135
NM_018026.4(PACS1):c.607C>T (p.Arg203Trp) rs398123009
NM_018116.4(MSTO1):c.1259del (p.Gly420fs) rs1248439783
NM_019098.5(CNGB3):c.391C>T (p.Gln131Ter) rs786204492
NM_020928.2(ZSWIM6):c.3487C>T (p.Arg1163Trp) rs587777695
NM_020975.6(RET):c.1947G>A (p.Ser649=) rs377767412
NM_152393.4(KLHL40):c.703G>T (p.Glu235Ter) rs768335581
Single allele

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