ClinVar Miner

Variants from Pathology and Clinical Laboratory Medicine, King Fahad Medical City with conflicting interpretations

Location: Saudi Arabia  Primary collection method: clinical testing
Minimum review status of the submission from Pathology and Clinical Laboratory Medicine, King Fahad Medical City: Collection method of the submission from Pathology and Clinical Laboratory Medicine, King Fahad Medical City:
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
104 52 0 55 7 1 19 77

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
Pathology and Clinical Laboratory Medicine, King Fahad Medical City pathogenic likely pathogenic uncertain significance likely benign other
pathogenic 0 28 8 0 0
likely pathogenic 24 0 6 1 0
uncertain significance 1 0 0 0 0
likely benign 0 1 3 0 0
benign 3 0 4 3 1

Submitter to submitter summary #

Total submitters: 57
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
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center 0 33 0 17 0 0 6 23
Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City 0 23 0 13 0 0 0 13
Baylor Genetics 0 29 0 9 1 0 1 11
Invitae 0 16 0 4 2 0 4 10
OMIM 0 30 0 7 0 0 1 8
Revvity Omics, Revvity 0 19 0 3 1 0 2 6
Counsyl 0 6 0 2 0 0 2 4
GeneDx 0 6 0 2 0 0 1 3
Centogene AG - the Rare Disease Company 0 3 0 2 0 0 1 3
Department Of Translational Genomics (developmental Genetics Section), King Faisal Specialist Hospital & Research Centre 0 1 0 2 0 0 1 3
Genome-Nilou Lab 0 8 0 3 0 0 0 3
3billion 0 7 0 1 0 0 2 3
Genetic Services Laboratory, University of Chicago 0 3 0 1 1 0 0 2
Genome Diagnostics Laboratory, University Medical Center Utrecht 0 4 0 1 0 0 1 2
Natera, Inc. 0 5 0 1 0 0 1 2
Eurofins Ntd Llc (ga) 0 2 0 0 1 1 0 2
Mayo Clinic Laboratories, Mayo Clinic 0 3 0 0 1 0 1 2
Fulgent Genetics, Fulgent Genetics 0 7 0 0 0 0 2 2
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) 0 0 0 2 0 0 0 2
CeGaT Center for Human Genetics Tuebingen 0 0 0 0 1 0 1 2
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ 0 1 0 2 0 0 0 2
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 3 0 1 0 0 1 2
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) 0 0 0 0 1 0 1 2
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 3 0 0 1 0 1 2
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 5 0 0 1 0 0 1
Molecular Diagnostics Lab, Nemours Children's Health, Delaware 0 0 0 1 0 0 0 1
Ambry Genetics 0 0 0 0 1 0 0 1
MGZ Medical Genetics Center 0 0 0 0 0 0 1 1
Centre for Inherited Metabolic Diseases, Karolinska University Hospital 0 1 0 0 0 0 1 1
MyeliNeuroGene Lab, McGill University Health Center Research Institute 0 0 0 0 0 0 1 1
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 6 0 1 0 0 0 1
Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München 0 3 0 0 0 0 1 1
Illumina Laboratory Services, Illumina 0 3 0 0 0 0 1 1
Centre for Translational Omics - GOSgene, University College London 0 0 0 1 0 0 0 1
Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine 0 1 0 1 0 0 0 1
Hadassah Hebrew University Medical Center 0 0 0 1 0 0 0 1
UW Hindbrain Malformation Research Program, University of Washington 0 2 0 1 0 0 0 1
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital 0 0 0 0 0 0 1 1
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics 0 0 0 0 1 0 0 1
Bioscientia Institut fuer Medizinische Diagnostik GmbH, Sonic Healthcare 0 1 0 1 0 0 0 1
Centre for Mendelian Genomics, University Medical Centre Ljubljana 0 1 0 0 0 0 1 1
Center for Molecular Medicine, Children’s Hospital of Fudan University 0 0 0 1 0 0 0 1
SIB Swiss Institute of Bioinformatics 0 1 0 0 0 0 1 1
Department of Pathology and Laboratory Medicine, Sinai Health System 0 0 0 0 0 0 1 1
Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine 0 1 0 1 0 0 0 1
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago 0 0 0 0 1 0 0 1
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen 0 0 0 0 0 0 1 1
Laboratory of Diagnosis and Therapy of Lysosomal Disorders, University of Padova 0 0 0 0 0 0 1 1
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard 0 1 0 0 0 0 1 1
Department of Biochemistry, Faculty of Medicine, University of Khartoum 0 1 0 0 0 0 1 1
Section for Clinical Neurogenetics, University of Tübingen 0 1 0 0 0 0 1 1
Institute of Human Genetics, University Hospital Muenster 0 0 0 0 0 0 1 1
AiLife Diagnostics, AiLife Diagnostics 0 0 0 0 0 0 1 1
Division Of Personalized Genomic Medicine, Columbia University Irving Medical Center 0 0 0 1 0 0 0 1
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 0 2 0 0 0 0 1 1
Henan Key Laboratory of Chronic Disease Management, Central China Fuwai Hospital of Zhengzhou University, Fuwai Central China Cardiovascular Hospital & Central China Branch of National Center for Cardiovascular Diseases 0 0 0 0 0 0 1 1
Clinical Laboratory Sciences Program (CLSP), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS) 0 8 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 77
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_002185.5(IL7R):c.197T>C (p.Ile66Thr) rs1494558 0.68368
NM_014694.4(ADAMTSL2):c.2313A>G (p.Val771=) rs1064975 0.61566
NM_014694.4(ADAMTSL2):c.1641C>T (p.His547=) rs7868941 0.16167
NM_000410.4(HFE):c.187C>G (p.His63Asp) rs1799945 0.10170
NM_005915.6(MCM6):c.2428T>C (p.Tyr810His) rs55660827 0.00036
NM_015846.4(MBD1):c.1304C>T (p.Thr435Ile) rs116201949 0.00035
NM_000151.4(G6PC1):c.247C>T (p.Arg83Cys) rs1801175 0.00034
NM_015426.5(POC1A):c.784C>T (p.Arg262Trp) rs146976547 0.00019
NM_000466.3(PEX1):c.627G>A (p.Met209Ile) rs200752969 0.00016
NM_006493.4(CLN5):c.448C>T (p.Arg150Ter) rs546989392 0.00010
NM_000183.3(HADHB):c.712C>T (p.Arg238Trp) rs764006338 0.00006
NM_025114.4(CEP290):c.5668G>T (p.Gly1890Ter) rs137852832 0.00006
NM_152268.4(PARS2):c.283G>A (p.Val95Ile) rs147227819 0.00005
NM_014141.6(CNTNAP2):c.3716-6C>G rs77025884 0.00004
NM_018668.5(VPS33B):c.1780A>G (p.Arg594Gly) rs868354713 0.00004
NM_001126108.2(SLC12A3):c.1844C>T (p.Ser615Leu) rs779160677 0.00003
NM_000181.4(GUSB):c.1429C>T (p.Arg477Trp) rs774393243 0.00002
NM_003401.5(XRCC4):c.127T>C (p.Trp43Arg) rs587779351 0.00002
NM_032861.4(SERAC1):c.202C>T (p.Arg68Ter) rs529232938 0.00002
NM_032861.4(SERAC1):c.442C>T (p.Arg148Ter) rs387907236 0.00002
NM_194293.4(XIRP1):c.4495G>A (p.Glu1499Lys) rs369082457 0.00002
NM_000094.4(COL7A1):c.4448G>A (p.Gly1483Asp) rs756217590 0.00001
NM_000320.3(QDPR):c.344C>T (p.Ser115Leu) rs1407920390 0.00001
NM_000340.2(SLC2A2):c.1250C>T (p.Pro417Leu) rs121909744 0.00001
NM_001040716.2(PC):c.806G>A (p.Arg269Gln) rs1349343839 0.00001
NM_001195518.2(MICU1):c.547C>T (p.Gln183Ter) rs777327250 0.00001
NM_001278716.2(FBXL4):c.292C>T (p.Arg98Ter) rs1554222130 0.00001
NM_001371986.1(UNC80):c.3787C>T (p.Arg1263Ter) rs864321622 0.00001
NM_003850.3(SUCLA2):c.1219C>T (p.Arg407Trp) rs1233249991 0.00001
NM_006031.6(PCNT):c.5767C>T (p.Arg1923Ter) rs119479062 0.00001
NM_013328.4(PYCR2):c.40G>C (p.Ala14Pro) rs1210762206 0.00001
NM_015713.5(RRM2B):c.204+5G>A rs372991229 0.00001
NM_138422.4(ADAT3):c.430G>A (p.Val144Met) rs730882213 0.00001
NM_000023.4(SGCA):c.226C>T (p.Leu76Phe) rs1555568335
NM_000123.4(ERCC5):c.2427del (p.Asp809fs) rs777455688
NM_000153.4(GALC):c.621G>A (p.Lys207=) rs1428763453
NM_000270.4(PNP):c.12-1G>C rs2139335095
NM_000270.4(PNP):c.437C>T (p.Pro146Leu) rs1594427504
NM_000271.5(NPC1):c.547G>A (p.Ala183Thr) rs111256741
NM_000277.3(PAH):c.671T>C (p.Ile224Thr) rs62507323
NM_000282.4(PCCA):c.2119-2A>G rs867315913
NM_000282.4(PCCA):c.425G>A (p.Gly142Asp) rs796052019
NM_000317.3(PTS):c.238A>G (p.Met80Val) rs1057517810
NM_000317.3(PTS):c.342C>G (p.Ile114Met) rs17851590
NM_000396.4(CTSK):c.830C>T (p.Ala277Val) rs74315304
NM_000443.4(ABCB4):c.2692G>A (p.Glu898Lys) rs1808782267
NM_000443.4(ABCB4):c.2906G>A (p.Arg969His) rs752916287
NM_000507.4(FBP1):c.114_119dup (p.Cys39_Thr40dup) rs1554682769
NM_000512.5(GALNS):c.1429_1455del (p.Glu477_Gln485del) rs1909818289
NM_001032386.2(SUOX):c.520del (p.Asp174fs) rs1565798380
NM_001077365.2(POMT1):c.1175+4_1175+7del rs1588409344
NM_001077365.2(POMT1):c.2113_2114del (p.Ser705fs) rs587777819
NM_001329.4(CTBP2):c.22A>T (p.Lys8Ter) rs76555439
NM_001371986.1(UNC80):c.409C>T (p.Arg137Ter) rs1289499829
NM_001378615.1(CC2D2A):c.3084del (p.Lys1029fs) rs386833749
NM_001378615.1(CC2D2A):c.4531T>C (p.Trp1511Arg) rs1721483506
NM_002778.4(PSAP):c.722G>C (p.Cys241Ser) rs121918104
NM_003193.5(TBCE):c.155_166del (p.Ser52_Gly55del) rs767004810
NM_003721.4(RFXANK):c.271+1G>C rs759667201
NM_003721.4(RFXANK):c.362A>T (p.Asp121Val) rs104894709
NM_005138.3(SCO2):c.2T>C (p.Met1Thr) rs1603441682
NM_005529.7(HSPG2):c.11208-7G>A rs1336552092
NM_006031.6(PCNT):c.398del (p.Phe133fs) rs1131691484
NM_007055.4(POLR3A):c.1771-7C>G rs201314157
NM_015046.7(SETX):c.6638C>T (p.Pro2213Leu) rs28940290
NM_015087.5(SPART):c.988A>G (p.Met330Val) rs1399213398
NM_016373.4(WWOX):c.606-1G>A rs730882215
NM_017777.4(MKS1):c.1126dup (p.Thr376fs) rs2143753386
NM_022356.4(P3H1):c.1839-2A>C rs755665899
NM_022356.4(P3H1):c.570_571del (p.Gly191fs) rs1553143741
NM_024570.4(RNASEH2B):c.356A>G (p.Asp119Gly) rs786205483
NM_025114.4(CEP290):c.5704G>T (p.Glu1902Ter) rs267606719
NM_033419.5(PGAP3):c.850C>T (p.His284Tyr) rs759541820
NM_058172.6(ANTXR2):c.134T>C (p.Leu45Pro) rs886041401
NM_133459.4(CCBE1):c.1079G>A (p.Arg360Gln) rs200219373
NM_152564.5(VPS13B):c.1219C>T (p.Gln407Ter) rs386834070
NM_178526.5(SLC25A42):c.871A>G (p.Asn291Asp) rs864321624

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