ClinVar Miner

Variants from Clinical Genomics Program, Stanford Medicine with conflicting interpretations

Location: United States  Primary collection method: clinical testing
Minimum review status of the submission from Clinical Genomics Program, Stanford Medicine: Collection method of the submission from Clinical Genomics Program, Stanford 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
109 53 0 25 13 4 15 46

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
Clinical Genomics Program, Stanford Medicine pathogenic likely pathogenic uncertain significance likely benign benign established risk allele pathogenic, low penetrance risk factor
pathogenic 0 19 6 0 1 0 3 0
likely pathogenic 6 0 2 0 0 0 0 0
uncertain significance 5 3 0 9 4 1 0 1

Submitter to submitter summary #

Total submitters: 58
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 37 0 1 11 3 3 18
OMIM 0 19 0 2 0 0 5 7
Institute of Human Genetics, University of Leipzig Medical Center 0 14 0 5 0 0 2 7
Baylor Genetics 0 18 0 3 0 0 2 5
Revvity Omics, Revvity 0 11 0 5 0 0 0 5
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center 0 4 0 4 0 0 0 4
Mendelics 0 12 0 1 0 0 2 3
Fulgent Genetics, Fulgent Genetics 0 8 0 3 0 0 0 3
Illumina Laboratory Services, Illumina 0 17 0 1 1 0 1 3
SIB Swiss Institute of Bioinformatics 0 0 0 3 0 0 0 3
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center 0 7 0 1 0 0 1 2
Elsea Laboratory, Baylor College of Medicine 0 1 0 0 0 0 2 2
MGZ Medical Genetics Center 0 10 0 2 0 0 0 2
Natera, Inc. 0 11 0 0 2 0 0 2
Centre for Mendelian Genomics, University Medical Centre Ljubljana 0 5 0 2 0 0 0 2
Al Jalila Children's Genomics Center, Al Jalila Childrens Speciality Hospital 0 1 0 0 2 0 0 2
Genome-Nilou Lab 0 11 0 1 0 0 1 2
3billion 0 10 0 1 0 0 1 2
Athena Diagnostics Inc 0 0 0 1 0 0 0 1
Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital 0 0 0 0 0 0 1 1
Genetic Services Laboratory, University of Chicago 0 6 0 0 0 0 1 1
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 2 0 1 0 0 0 1
GeneDx 0 2 0 1 0 0 0 1
Counsyl 0 2 0 0 0 0 1 1
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 16 0 1 0 0 0 1
Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine 0 2 0 1 0 0 0 1
Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München 0 7 0 1 0 0 0 1
LDLR-LOVD, British Heart Foundation 0 1 0 1 0 0 0 1
Genomic Research Center, Shahid Beheshti University of Medical Sciences 0 3 0 1 0 0 0 1
UCLA Clinical Genomics Center, UCLA 0 0 0 0 0 0 1 1
Division of Human Genetics, Children's Hospital of Philadelphia 0 2 0 1 0 0 0 1
Knight Diagnostic Laboratories, Oregon Health and Sciences University 0 6 0 0 0 0 1 1
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics 0 0 0 0 0 0 1 1
Laboratory of Genetics and Molecular Cardiology, University of São Paulo 0 0 0 1 0 0 0 1
Center of Genomic medicine, Geneva, University Hospital of Geneva 0 2 0 0 0 1 0 1
Institute of Human Genetics, University Hospital of Duesseldorf 0 0 0 1 0 0 0 1
Robarts Research Institute, Western University 0 0 0 1 0 0 0 1
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne 0 5 0 1 0 0 0 1
Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation 0 0 0 1 0 0 0 1
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego 0 2 0 0 0 0 1 1
Department of Pathology and Laboratory Medicine, Sinai Health System 0 0 0 0 0 1 0 1
Laboratoire de Génétique Moléculaire, CHU Bordeaux 0 0 0 1 0 0 0 1
Fundacion Hipercolesterolemia Familiar 0 1 0 1 0 0 0 1
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen 0 1 0 0 0 0 1 1
SingHealth Duke-NUS Institute of Precision Medicine 0 0 0 0 0 0 1 1
Génétique des Maladies du Développement, Hospices Civils de Lyon 0 1 0 1 0 0 0 1
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard 0 3 0 1 0 0 0 1
UNC Molecular Genetics Laboratory, University of North Carolina at Chapel Hill 0 4 0 1 0 0 0 1
Laboratory of Medical Genetics, National & Kapodistrian University of Athens 0 2 0 0 0 0 1 1
Department of Genetics, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine 0 1 0 1 0 0 0 1
Zotz-Klimas Genetics Lab, MVZ Zotz Klimas 0 3 0 1 0 0 0 1
Autoinflammatory diseases unit, CHU de Montpellier 0 1 0 1 0 0 0 1
Institute of Human Genetics, Clinical Exome/Genome Diagnostics Group, University Hospital Bonn 0 1 0 0 0 0 1 1
Suma Genomics 0 2 0 0 0 0 1 1
Genomics England Pilot Project, Genomics England 0 2 0 1 0 0 0 1
Molecular Genetics, Royal Melbourne Hospital 0 3 0 1 0 0 0 1
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 0 6 0 0 0 0 1 1
Giacomini Lab, University of California, San Francisco 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 46
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000410.4(HFE):c.187C>G (p.His63Asp) rs1799945 0.10170
NM_000036.3(AMPD1):c.143C>T (p.Pro48Leu) rs61752479 0.08857
NM_000036.3(AMPD1):c.34C>T (p.Gln12Ter) rs17602729 0.08701
NM_000410.4(HFE):c.845G>A (p.Cys282Tyr) rs1800562 0.03880
NM_001370658.1(BTD):c.1270G>C (p.Asp424His) rs13078881 0.03225
NM_005105.5(RBM8A):c.-21G>A rs139428292 0.01871
NM_000036.3(AMPD1):c.1224+8G>A rs140176911 0.01045
NM_012452.3(TNFRSF13B):c.310T>C (p.Cys104Arg) rs34557412 0.00403
NM_000036.3(AMPD1):c.930G>T (p.Met310Ile) rs61752478 0.00384
NM_003119.4(SPG7):c.1529C>T (p.Ala510Val) rs61755320 0.00361
NM_001089.3(ABCA3):c.875A>T (p.Glu292Val) rs149989682 0.00304
NM_001243279.3(ACSF3):c.1672C>T (p.Arg558Trp) rs141090143 0.00278
NM_000155.4(GALT):c.563A>G (p.Gln188Arg) rs75391579 0.00192
NM_001845.6(COL4A1):c.1000-5T>G rs75711155 0.00155
NM_001378454.1(ALMS1):c.2036A>G (p.Tyr679Cys) rs199573929 0.00146
NM_024570.4(RNASEH2B):c.529G>A (p.Ala177Thr) rs75184679 0.00141
NM_003060.4(SLC22A5):c.1345T>G (p.Tyr449Asp) rs11568514 0.00114
NM_001378454.1(ALMS1):c.11070C>T (p.Gly3690=) rs371329585 0.00023
NM_000432.4(MYL2):c.37G>A (p.Ala13Thr) rs104894363 0.00020
NM_017636.4(TRPM4):c.2133-9C>G rs530013543 0.00009
NM_001134363.3(RBM20):c.2116C>A (p.Pro706Thr) rs373797219 0.00007
NM_033380.3(COL4A5):c.1871G>A (p.Gly624Asp) rs104886142 0.00005
NM_014704.4(CEP104):c.2662+10A>T rs552644535 0.00004
NM_003060.4(SLC22A5):c.453G>A (p.Val151=) rs386134194 0.00003
NM_001134363.3(RBM20):c.2333C>T (p.Ala778Val) rs397516602 0.00002
NM_001199107.2(TBC1D24):c.845C>G (p.Pro282Arg) rs747538224 0.00002
NM_005138.3(SCO2):c.268C>T (p.Arg90Ter) rs74315512 0.00002
NM_006939.4(SOS2):c.2350C>T (p.Arg784Cys) rs760520078 0.00002
NM_020975.6(RET):c.2370G>T (p.Leu790Phe) rs75030001 0.00001
NM_000256.3(MYBPC3):c.3628-41_3628-17del rs36212066
NM_000527.5(LDLR):c.1897C>T (p.Arg633Cys)
NM_000548.5(TSC2):c.225+2T>C rs397515105
NM_000834.5(GRIN2B):c.2477G>A (p.Gly826Glu) rs1064794979
NM_001011.4(RPS7):c.-19+1G>A rs1064796859
NM_001127222.2(CACNA1A):c.4072C>T (p.Arg1358Trp) rs1555745461
NM_001318852.2(MAPK8IP3):c.1735C>T (p.Arg579Cys) rs1567203083
NM_002074.5(GNB1):c.233A>G (p.Lys78Arg) rs869312823
NM_002074.5(GNB1):c.239T>C (p.Ile80Thr) rs752746786
NM_003091.4(SNRPB):c.155+301G>C rs786201019
NM_006245.4(PPP2R5D):c.598G>A (p.Glu200Lys) rs863225079
NM_007118.4(TRIO):c.4394A>G (p.Asn1465Ser) rs1747669042
NM_007327.4(GRIN1):c.2530C>T (p.Arg844Cys) rs1554770667
NM_016284.5(CNOT1):c.4432C>T (p.Arg1478Cys) rs1567396193
NM_016628.5(WAC):c.381+4_381+7del rs1564400647
NM_078480.3(PUF60):c.612_630del (p.Asn207fs) rs1816565452
NM_177559.3(CSNK2A1):c.593A>G (p.Lys198Arg) rs869312840

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.