ClinVar Miner

Variants from Clinical Laboratory Sciences Program (CLSP), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS) with conflicting interpretations

Location: Saudi Arabia  Primary collection method: clinical testing
Minimum review status of the submission from Clinical Laboratory Sciences Program (CLSP), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS): Collection method of the submission from Clinical Laboratory Sciences Program (CLSP), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS):
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
80 60 0 58 1 0 15 67

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 Laboratory Sciences Program (CLSP), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS) pathogenic likely pathogenic uncertain significance likely benign
pathogenic 0 42 5 0
likely pathogenic 16 0 6 0
uncertain significance 4 1 0 1

Submitter to submitter summary #

Total submitters: 53
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 31 0 8 0 0 5 13
Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City 0 14 0 11 0 0 0 11
Baylor Genetics 0 38 0 8 0 0 1 9
Counsyl 0 8 0 6 0 0 2 8
Invitae 0 33 0 7 1 0 0 8
OMIM 0 39 0 3 0 0 2 5
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard 0 1 0 3 0 0 1 4
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 9 0 3 0 0 0 3
Centogene AG - the Rare Disease Company 0 7 0 3 0 0 0 3
3billion 0 18 0 2 0 0 1 3
Revvity Omics, Revvity 0 17 0 2 0 0 0 2
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 15 0 2 0 0 0 2
Mendelics 0 5 0 2 0 0 0 2
Illumina Laboratory Services, Illumina 0 7 0 1 0 0 1 2
UCLA Clinical Genomics Center, UCLA 0 0 0 2 0 0 0 2
Centre of Medical Genetics, University of Antwerp 0 0 0 2 0 0 0 2
Institute of Human Genetics, University of Leipzig Medical Center 0 12 0 2 0 0 0 2
SIB Swiss Institute of Bioinformatics 0 1 0 2 0 0 0 2
Department Of Genetics, Sultan Qaboos University Hospital, Sultan Qaboos University 0 3 0 1 0 0 1 2
Genome-Nilou Lab 0 13 0 2 0 0 0 2
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 0 4 0 2 0 0 0 2
Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital 0 6 0 0 0 0 1 1
Genetic Services Laboratory, University of Chicago 0 4 0 1 0 0 0 1
Molecular Diagnostics Lab, Nemours Children's Health, Delaware 0 0 0 1 0 0 0 1
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia 0 2 0 1 0 0 0 1
Intergen, Intergen Genetics and Rare Diseases Diagnosis Center 0 3 0 1 0 0 0 1
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 0 9 0 1 0 0 0 1
Fulgent Genetics, Fulgent Genetics 0 14 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 0 0 0 1 1
Blueprint Genetics 0 0 0 1 0 0 0 1
Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München 0 6 0 1 0 0 0 1
Center for Medical Genetics Ghent, University of Ghent 0 0 0 1 0 0 0 1
Centre for Translational Omics - GOSgene, University College London 0 0 0 1 0 0 0 1
UW Hindbrain Malformation Research Program, University of Washington 0 0 0 1 0 0 0 1
Oxford Medical Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust 0 1 0 1 0 0 0 1
Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India 0 3 0 1 0 0 0 1
NIHR Bioresource Rare Diseases, University of Cambridge 0 0 0 1 0 0 0 1
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne 0 4 0 1 0 0 0 1
Génétique des Maladies du Développement, Hospices Civils de Lyon 0 2 0 1 0 0 0 1
Laboratory of Medical Genetics, National & Kapodistrian University of Athens 0 2 0 1 0 0 0 1
Laboratory of Medical Genetics, University of Torino 0 1 0 1 0 0 0 1
Cavalleri Lab, Royal College of Surgeons in Ireland 0 0 0 1 0 0 0 1
Pathology and Clinical Laboratory Medicine, King Fahad Medical City 0 8 0 1 0 0 0 1
Johns Hopkins Genomics, Johns Hopkins University 0 5 0 1 0 0 0 1
Myriad Genetics, Inc. 0 5 0 0 0 0 1 1
New York Genome Center 0 6 0 1 0 0 0 1
Lifecell International Pvt. Ltd 0 4 0 1 0 0 0 1
ISTH-SSC Genomics in Thrombosis and Hemostasis, KU Leuven, Center for Molecular and Vascular Biology 0 0 0 1 0 0 0 1
DASA 0 6 0 1 0 0 0 1
Neuberg Centre For Genomic Medicine, NCGM 0 6 0 1 0 0 0 1
Molecular Genetics, Royal Melbourne Hospital 0 0 0 1 0 0 0 1
Dunham Lab, University of Washington 0 2 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 67
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000402.4(G6PD):c.292G>A (p.Val98Met) rs1050828 0.03616
NM_016335.6(PRODH):c.1322T>C (p.Leu441Pro) rs2904551 0.00282
NM_007055.4(POLR3A):c.1909+22G>A rs191875469 0.00156
NM_000155.4(GALT):c.404C>T (p.Ser135Leu) rs111033690 0.00094
NM_001182.5(ALDH7A1):c.1279G>C (p.Glu427Gln) rs121912707 0.00024
NM_001038.6(SCNN1A):c.340G>A (p.Val114Ile) rs61759861 0.00018
NM_001385.3(DPYS):c.1137C>A (p.Ser379Arg) rs201258823 0.00016
NM_183050.4(BCKDHB):c.853C>T (p.Arg285Ter) rs398124598 0.00015
NM_000551.4(VHL):c.598C>T (p.Arg200Trp) rs28940298 0.00010
NM_007103.4(NDUFV1):c.1157G>A (p.Arg386His) rs536758576 0.00009
NM_001017420.3(ESCO2):c.1132-7A>G rs80359862 0.00007
NM_019616.4(F7):c.845C>T (p.Ala282Val) rs121964931 0.00006
NM_022464.5(SIL1):c.1030-9G>A rs370290043 0.00006
NM_000363.5(TNNI3):c.484C>T (p.Arg162Trp) rs368861241 0.00004
NM_000402.4(G6PD):c.1039G>A (p.Glu347Lys) rs137852339 0.00004
NM_000155.4(GALT):c.200G>A (p.Arg67His) rs758430398 0.00003
NM_000402.4(G6PD):c.1093G>A (p.Ala365Thr) rs5030869 0.00003
NM_138425.4(C12orf57):c.1A>G (p.Met1Val) rs587776954 0.00003
NM_032861.4(SERAC1):c.442C>T (p.Arg148Ter) rs387907236 0.00002
NM_000048.4(ASL):c.332G>A (p.Arg111Gln) rs561367199 0.00001
NM_000053.4(ATP7B):c.51+4A>T rs369488210 0.00001
NM_000429.3(MAT1A):c.595C>T (p.Arg199Cys) rs773267230 0.00001
NM_001082971.2(DDC):c.1234C>T (p.Arg412Trp) rs542063660 0.00001
NM_003560.4(PLA2G6):c.1933C>T (p.Arg645Ter) rs1484455290 0.00001
NM_000059.4(BRCA2):c.7007G>A (p.Arg2336His) rs28897743
NM_000071.3(CBS):c.457G>A (p.Gly153Arg) rs745704046
NM_000071.3(CBS):c.969G>A (p.Trp323Ter) rs863223432
NM_000138.5(FBN1):c.2051G>A (p.Cys684Tyr) rs1555399763
NM_000138.5(FBN1):c.3656A>G (p.Tyr1219Cys) rs1555398394
NM_000142.5(FGFR3):c.1620C>G (p.Asn540Lys) rs28933068
NM_000142.5(FGFR3):c.749C>G (p.Pro250Arg) rs4647924
NM_000155.4(GALT):c.997C>T (p.Arg333Trp) rs111033800
NM_000277.3(PAH):c.833C>A (p.Thr278Asn) rs62507262
NM_000282.4(PCCA):c.425G>A (p.Gly142Asp) rs796052019
NM_000284.4(PDHA1):c.1142_1145dup (p.Trp383fs) rs606231189
NM_000348.4(SRD5A2):c.282-2A>G rs1340425455
NM_000392.5(ABCC2):c.2273G>T (p.Gly758Val) rs786205465
NM_000414.4(HSD17B4):c.2029C>T (p.Gln677Ter) rs751646311
NM_000521.4(HEXB):c.1169+3_1169+10del rs398123444
NM_001034850.3(RETREG1):c.926C>G (p.Ser309Ter) rs137852739
NM_001039591.3(USP9X):c.90G>C (p.Gln30His)
NM_001042492.3(NF1):c.7909C>T (p.Arg2637Ter) rs786201367
NM_001110792.2(MECP2):c.509C>T (p.Thr170Met) rs28934906
NM_001130438.3(SPTAN1):c.6616GAG[1] (p.Glu2207del) rs587784438
NM_001134232.2(TMEM106B):c.754G>A (p.Asp252Asn) rs1554310600
NM_001171613.2(PREPL):c.1366C>T (p.Gln456Ter) rs1673549822
NM_001356.5(DDX3X):c.830_831del (p.Glu277fs) rs1602131859
NM_001372044.2(SHANK3):c.3952dup (p.Gln1318fs)
NM_001378615.1(CC2D2A):c.3364C>T (p.Pro1122Ser) rs118204051
NM_001399.5(EDA):c.760C>T (p.Gln254Ter)
NM_003193.5(TBCE):c.155_166del (p.Ser52_Gly55del) rs767004810
NM_003664.5(AP3B1):c.364C>T (p.Arg122Ter)
NM_014236.4(GNPAT):c.569-3T>G rs745869264
NM_015100.4(POGZ):c.3259C>T (p.Arg1087Ter) rs879255404
NM_018026.4(PACS1):c.607C>T (p.Arg203Trp) rs398123009
NM_021939.4(FKBP10):c.831dup (p.Gly278fs) rs137853883
NM_024685.4(BBS10):c.728_731del (p.Lys243fs) rs786204671
NM_033419.5(PGAP3):c.850C>T (p.His284Tyr) rs759541820
NM_052988.5(CDK10):c.139del (p.Glu47fs) rs1555516716
NM_057175.5(NAA15):c.2344C>T (p.Arg782Ter) rs1270628305
NM_058172.6(ANTXR2):c.134T>C (p.Leu45Pro) rs886041401
NM_138376.3(TTC5):c.418C>T (p.Gln140Ter)
NM_138775.3(ALKBH8):c.1651C>T (p.Arg551Ter) rs375189195
NM_152281.3(GORAB):c.231dup (p.Pro78fs) rs1571243797
NM_178161.3(PTF1A):c.571C>A (p.Pro191Thr) rs1588563037
NM_178526.5(SLC25A42):c.871A>G (p.Asn291Asp) rs864321624
NM_198239.2(CCN6):c.246del (p.Glu84fs) rs797044438

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