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:

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
83 57 0 71 7 1 22 93

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 32 8 0 0
likely pathogenic 28 0 10 1 0
uncertain significance 1 0 0 0 0
likely benign 0 1 3 0 0
benign 2 0 4 11 1

Submitter to submitter summary #

Total submitters: 68
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
Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre 0 46 0 23 0 0 10 33
Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City 0 23 0 13 0 0 0 13
Labcorp Genetics (formerly Invitae), Labcorp 0 16 0 4 2 0 5 11
Baylor Genetics 0 31 0 8 0 0 1 9
Breakthrough Genomics, Breakthrough Genomics 0 6 0 8 0 0 0 8
OMIM 0 30 0 7 0 0 0 7
Revvity Omics, Revvity 0 21 0 4 1 0 2 7
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 12 0 5 1 0 0 6
3billion 0 13 0 2 0 0 2 4
Counsyl 0 6 0 2 0 0 2 4
Fulgent Genetics, Fulgent Genetics 0 10 0 2 0 0 2 4
GeneDx 0 6 0 2 1 0 1 4
Natera, Inc. 0 9 0 3 0 0 1 4
CENTOGENE GmbH and LLC - Guiding Precision Medicine 0 3 0 2 0 0 1 3
Genome-Nilou Lab 0 8 0 3 0 0 0 3
Mayo Clinic Laboratories, Mayo Clinic 0 6 0 0 2 0 1 3
CeGaT Center for Human Genetics Tuebingen 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
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 3 0 1 0 0 1 2
Eurofins Ntd Llc (ga) 0 2 0 0 1 1 0 2
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
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ 0 1 0 2 0 0 0 2
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) 0 0 0 2 0 0 0 2
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) 0 0 0 0 1 0 1 2
Neuberg Centre For Genomic Medicine, NCGM 0 2 0 0 0 0 2 2
AiLife Diagnostics, AiLife Diagnostics 0 0 0 0 0 0 1 1
Ambry Genetics 0 0 0 0 1 0 0 1
Bioscientia Institut fuer Medizinische Diagnostik GmbH, Sonic Healthcare 0 2 0 1 0 0 0 1
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard 0 1 0 0 0 0 1 1
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital 0 0 0 0 0 0 1 1
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago 0 0 0 0 1 0 0 1
Center for Molecular Medicine, Children’s Hospital of Fudan University 0 0 0 1 0 0 0 1
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics 0 0 0 0 1 0 0 1
Centre for Inherited Metabolic Diseases, Karolinska University Hospital 0 1 0 0 0 0 1 1
Centre for Mendelian Genomics, University Medical Centre Ljubljana 0 1 0 0 0 0 1 1
Centre for Translational Omics - GOSgene, University College London 0 0 0 1 0 0 0 1
Centre of Medical Genetics, University Hospital Muenster 0 0 0 0 0 0 1 1
Clinical Genetics Laboratory, Skane University Hospital Lund 0 1 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
Dasa 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
Department of Pathology and Laboratory Medicine, Sinai Health System 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
First Genomix Gene Laboratory, Genetic Diagnostics Department 0 2 0 1 0 0 0 1
Genetics and Genomic Medicine Centre, NeuroGen Healthcare, NeuroGen Healthcare 0 0 0 1 0 0 0 1
Hadassah Hebrew University Medical Center 0 0 0 1 0 0 0 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
Illumina Laboratory Services, Illumina 0 3 0 0 0 0 1 1
Institute of Human Genetics Munich, TUM University Hospital 0 3 0 0 0 0 1 1
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen 0 1 0 0 0 0 1 1
Juno Genomics, Hangzhou Juno Genomics, Inc 0 1 0 1 0 0 0 1
Kariminejad - Najmabadi Pathology & Genetics Center 0 0 0 1 0 0 0 1
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 0 3 0 0 0 0 1 1
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 5 0 0 1 0 0 1
Laboratory of Diagnosis and Therapy of Lysosomal Disorders, University of Padova 0 0 0 0 0 0 1 1
Laboratory of Genetics, Children's Clinical University Hospital Latvia 0 2 0 0 0 0 1 1
Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine 0 1 0 1 0 0 0 1
MGZ Medical Genetics Center 0 0 0 0 0 0 1 1
Medical and Scientific Branch, Hong Kong Genome Institute 0 0 0 1 0 0 0 1
Molecular Diagnostics Lab, Nemours Children's Health, Delaware 0 2 0 1 0 0 0 1
MyeliNeuroGene Lab, McGill University Health Center Research Institute 0 0 0 0 0 0 1 1
SIB Swiss Institute of Bioinformatics 0 1 0 0 0 0 1 1
Section for Clinical Neurogenetics, University of Tübingen 0 1 0 0 0 0 1 1
UW Hindbrain Malformation Research Program, University of Washington 0 2 0 1 0 0 0 1
Undiagnosed Diseases Network, NIH 0 0 0 0 0 0 1 1
Variantyx, Inc. 0 2 0 1 0 0 0 1
Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine 0 1 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 93
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_007293.3(C4A):c.2944+55T>C rs149464899 1.00000
NM_002185.5(IL7R):c.197T>C (p.Ile66Thr) rs1494558 0.68368
NM_014694.4(ADAMTSL2):c.2313A>G (p.Val771=) rs1064975 0.60212
NM_014694.4(ADAMTSL2):c.1641C>T (p.His547=) rs7868941 0.15561
NM_000410.4(HFE):c.187C>G (p.His63Asp) rs1799945 0.10170
NM_001270974.2(HYDIN):c.2768+22G>A rs6499399 0.00044
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_152268.4(PARS2):c.283G>A (p.Val95Ile) rs147227819 0.00009
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_001126108.2(SLC12A3):c.1844C>T (p.Ser615Leu) rs779160677 0.00003
NM_014141.6(CNTNAP2):c.3716-6C>G rs77025884 0.00003
NM_018668.5(VPS33B):c.1780A>G (p.Arg594Gly) rs868354713 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_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.2278C>T (p.Arg760Trp) rs563526275 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_001352514.2(HLCS):c.1963C>T (p.Arg655Trp) rs119103229 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_005529.7(HSPG2):c.11208-7G>A rs1336552092 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_032861.4(SERAC1):c.442C>T (p.Arg148Ter) rs387907236 0.00001
NM_138422.4(ADAT3):c.430G>A (p.Val144Met) rs730882213 0.00001
NM_194293.4(XIRP1):c.4495G>A (p.Glu1499Lys) rs369082457 0.00001
NM_198321.4(GALNT10):c.263-138A>T rs59278572 0.00001
NM_000023.4(SGCA):c.226C>T (p.Leu76Phe) rs1555568335
NM_000123.4(ERCC5):c.2427del (p.Asp809fs) rs777455688
NM_000152.5(GAA):c.896T>C (p.Leu299Pro) rs121907940
NM_000153.4(GALC):c.621G>A (p.Lys207=) rs1428763453
NM_000181.4(GUSB):c.1832G>A (p.Arg611Gln) rs1583879945
NM_000255.4(MMUT):c.810_811delinsA (p.Ala271fs) rs1767682543
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_001270974.2(HYDIN):c.12129+60G>A rs1798319
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_005026.5(PIK3CD):c.-138+2682G>C rs201016347
NM_005138.3(SCO2):c.2T>C (p.Met1Thr) rs1603441682
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_015702.3(MMADHC):c.702dup (p.Gly235fs) rs1682617973
NM_016373.4(WWOX):c.606-1G>A rs730882215
NM_017613.4(DONSON):c.786-22A>G rs1135401960
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_032861.4(SERAC1):c.308_311del (p.Arg103fs) rs1785136807
NM_033419.5(PGAP3):c.850C>T (p.His284Tyr) rs759541820
NM_058172.6(ANTXR2):c.134T>C (p.Leu45Pro) rs886041401
NM_058172.6(ANTXR2):c.720del (p.Ser240fs) rs1732803804
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
NM_183050.4(BCKDHB):c.1144T>C (p.Cys382Arg) rs727503822
NM_198321.4(GALNT10):c.263-139G>C rs57541779

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