ClinVar Miner

Variants from ClinVar Staff, National Center for Biotechnology Information (NCBI) with conflicting interpretations

Location: United States  Primary collection method: literature only
Minimum review status of the submission from ClinVar Staff, National Center for Biotechnology Information (NCBI): Collection method of the submission from ClinVar Staff, National Center for Biotechnology Information (NCBI):
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
734 375 0 23 2 0 30 51

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
ClinVar Staff, National Center for Biotechnology Information (NCBI) pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 1 1 0 0
likely pathogenic 21 0 3 1 1
uncertain significance 12 19 0 2 1
likely benign 0 0 0 0 1

Submitter to submitter summary #

Total submitters: 54
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
OMIM 0 27 0 21 0 0 7 28
Invitae 0 200 0 2 2 0 18 22
Baylor Genetics 0 15 0 3 0 0 13 16
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 60 0 1 0 0 7 8
Genome-Nilou Lab 0 61 0 1 0 0 6 7
Revvity Omics, Revvity 0 5 0 1 0 0 3 4
Natera, Inc. 0 31 0 0 0 0 4 4
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 0 1 0 1 0 0 2 3
Fulgent Genetics, Fulgent Genetics 0 7 0 1 0 0 2 3
Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München 0 1 0 3 0 0 0 3
3billion 0 4 0 2 0 0 1 3
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center 0 0 0 0 0 0 2 2
MGZ Medical Genetics Center 0 1 0 0 0 0 2 2
Genome Diagnostics Laboratory, University Medical Center Utrecht 0 2 0 1 1 0 0 2
Counsyl 0 87 0 0 0 0 2 2
Centre for Mendelian Genomics, University Medical Centre Ljubljana 0 3 0 2 0 0 0 2
Institute of Human Genetics, University of Leipzig Medical Center 0 76 0 1 0 0 1 2
Wangler Lab, Baylor College of Medicine 0 0 0 2 0 0 0 2
Myriad Genetics, Inc. 0 0 0 0 0 0 2 2
DASA 0 0 0 1 0 0 1 2
Genetic Services Laboratory, University of Chicago 0 1 0 1 0 0 0 1
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 6 0 0 0 0 1 1
Molecular Genetics Laboratory, BC Children's and BC Women's Hospitals 0 1 0 0 0 0 1 1
Centogene AG - the Rare Disease Company 0 1 0 1 0 0 0 1
Mendelics 0 30 0 0 0 0 1 1
Illumina Laboratory Services, Illumina 0 6 0 0 0 0 1 1
Department of Medical Genetics, Oslo University Hospital 0 0 0 0 0 0 1 1
Service de Génétique Moléculaire, Hôpital Robert Debré 0 0 0 1 0 0 0 1
Division of Human Genetics, Children's Hospital of Philadelphia 0 0 0 0 0 0 1 1
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology 0 0 0 1 0 0 0 1
Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille 0 0 0 1 0 0 0 1
Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center 0 1 0 0 0 0 1 1
Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India 0 2 0 1 0 0 0 1
Daryl Scott Lab, Baylor College of Medicine 0 0 0 1 0 0 0 1
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne 0 0 0 1 0 0 0 1
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego 0 1 0 1 0 0 0 1
Genome Diagnostics Laboratory, Amsterdam University Medical Center 0 0 0 1 0 0 0 1
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 0 0 0 1 0 0 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 0 0 1 0 0 0 1
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard 0 0 0 0 1 0 0 1
Laboratory of Medical Genetics, University of Torino 0 0 0 1 0 0 0 1
Breda Genetics srl 0 0 0 1 0 0 0 1
Johns Hopkins Genomics, Johns Hopkins University 0 41 0 1 0 0 0 1
Clinical Genetics Laboratory, Federal University of Health Sciences of Porto Alegre 0 0 0 0 0 0 1 1
Genetic Testing Center for Deafness, Department of Otolaryngology Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital 0 0 0 1 0 0 0 1
Department of Paediatrics and Adolescent Medicine, The University of Hong Kong 0 0 0 1 0 0 0 1
New York Genome Center 0 1 0 1 0 0 0 1
GenomeConnect - Simons Searchlight 0 0 0 1 0 0 0 1
Pediatric Genetics Clinic, Sheba Medical Center 0 0 0 1 0 0 0 1
Neuberg Centre For Genomic Medicine, NCGM 0 2 0 1 0 0 0 1
Genomics England Pilot Project, Genomics England 0 0 0 1 0 0 0 1
Eurofins-Biomnis 0 0 0 1 0 0 0 1
Clinical Laboratory Sciences Program (CLSP), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS) 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 51
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_032578.4(MYPN):c.3335C>T (p.Pro1112Leu) rs71534278 0.00318
NM_001111.5(ADAR):c.577C>G (p.Pro193Ala) rs145588689 0.00162
NM_032578.4(MYPN):c.59A>G (p.Tyr20Cys) rs140148105 0.00130
NM_032578.4(MYPN):c.3481C>A (p.Leu1161Ile) rs138313730 0.00123
NM_000528.4(MAN2B1):c.2426T>C (p.Leu809Pro) rs80338681 0.00006
NM_000435.3(NOTCH3):c.451C>G (p.Gln151Glu) rs371491165 0.00005
NM_000153.4(GALC):c.2041G>A (p.Val681Met) rs200607029 0.00004
NM_032578.4(MYPN):c.1229T>C (p.Val410Ala) rs199476406 0.00004
NM_000528.4(MAN2B1):c.1204G>A (p.Glu402Lys) rs370760999 0.00003
NM_012208.4(HARS2):c.598C>G (p.Leu200Val) rs397515410 0.00003
NM_000528.4(MAN2B1):c.2140T>C (p.Trp714Arg) rs864621993 0.00002
NM_000528.4(MAN2B1):c.2867T>G (p.Leu956Arg) rs768233248 0.00002
NM_000528.4(MAN2B1):c.1067C>G (p.Pro356Arg) rs121434333 0.00001
NM_000528.4(MAN2B1):c.1259G>T (p.Gly420Val) rs772853856 0.00001
NM_000528.4(MAN2B1):c.1351G>T (p.Gly451Cys) rs368899357 0.00001
NM_000528.4(MAN2B1):c.222C>A (p.Asp74Glu) rs746702002 0.00001
NM_000528.4(MAN2B1):c.598C>A (p.His200Asn) rs772108001 0.00001
NM_000528.4(MAN2B1):c.685C>T (p.Arg229Trp) rs763257568 0.00001
NM_000528.4(MAN2B1):c.788C>T (p.Pro263Leu) rs746808159 0.00001
NM_004700.4(KCNQ4):c.961G>A (p.Gly321Ser) rs28939710 0.00001
NM_152490.5(B3GALNT2):c.740G>A (p.Gly247Glu) rs367543072 0.00001
NM_152490.5(B3GALNT2):c.802G>A (p.Val268Met) rs367543074 0.00001
NM_000528.4(MAN2B1):c.1055T>C (p.Leu352Pro) rs864621980
NM_000528.4(MAN2B1):c.1358C>T (p.Ser453Phe) rs864621984
NM_000528.4(MAN2B1):c.164G>T (p.Cys55Phe) rs864621975
NM_000528.4(MAN2B1):c.215A>T (p.His72Leu) rs387906261
NM_000528.4(MAN2B1):c.2248C>T (p.Arg750Trp) rs80338680
NM_000528.4(MAN2B1):c.2398G>C (p.Gly800Arg) rs398123456
NM_000528.4(MAN2B1):c.2402G>A (p.Gly801Asp) rs864621994
NM_000528.4(MAN2B1):c.2747G>A (p.Arg916His) rs758765126
NM_000528.4(MAN2B1):c.2999T>C (p.Phe1000Ser) rs864621991
NM_000528.4(MAN2B1):c.590C>G (p.Pro197Arg) rs864621977
NM_001111.5(ADAR):c.2608G>A (p.Ala870Thr) rs398122893
NM_001111.5(ADAR):c.2615T>C (p.Ile872Thr) rs398122897
NM_001111.5(ADAR):c.2675G>A (p.Arg892His) rs398122892
NM_001111.5(ADAR):c.2997G>T (p.Lys999Asn) rs398122896
NM_001111.5(ADAR):c.3019G>A (p.Gly1007Arg) rs398122822
NM_001111.5(ADAR):c.3335A>T (p.Tyr1112Phe) rs398122895
NM_001111.5(ADAR):c.3337G>C (p.Asp1113His) rs398122894
NM_001312909.2(FAM111A):c.1012A>G (p.Thr338Ala) rs587777014
NM_001312909.2(FAM111A):c.1531T>C (p.Tyr511His) rs587777012
NM_001312909.2(FAM111A):c.1579C>A (p.Pro527Thr) rs587777015
NM_001312909.2(FAM111A):c.1583A>G (p.Asp528Gly) rs587777013
NM_001312909.2(FAM111A):c.1706G>A (p.Arg569His) rs587777011
NM_003441.4(ZNF141):c.1421C>T (p.Thr474Ile) rs587776959
NM_012208.4(HARS2):c.1102G>T (p.Val368Leu) rs376177973
NM_018026.4(PACS1):c.607C>T (p.Arg203Trp) rs398123009
NM_032578.4(MYPN):c.2882C>T (p.Pro961Leu) rs864621995
NM_052845.4(MMAB):c.56_57delinsAA (p.Arg19Gln) rs36013132
NM_152490.5(B3GALNT2):c.755T>G (p.Val252Gly) rs367543073
NM_152490.5(B3GALNT2):c.875G>C (p.Arg292Pro) rs367543076

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