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
98 34 1 30 1 1 6 36

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 1 15 3 0 0
likely pathogenic 14 0 1 0 0
uncertain significance 1 0 0 0 0
benign 1 0 1 1 1

Submitter to submitter summary #

Total submitters: 27
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
Biochemical Molecular Genetic Laboratory,King Abdulaziz Medical City 0 21 0 10 0 0 0 10
Baylor Genetics 0 21 0 6 0 0 1 7
OMIM 0 22 0 6 0 0 0 6
Counsyl 0 4 0 2 0 0 2 4
Invitae 0 7 0 2 0 0 1 3
Centogene AG - the Rare Disease Company 0 1 0 1 0 0 1 2
GeneReviews 0 5 1 1 0 0 0 2
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) 0 0 0 2 0 0 0 2
Genetic Services Laboratory, University of Chicago 0 3 0 1 0 0 0 1
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine 0 3 0 0 1 0 0 1
GeneDx 0 1 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
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics 0 1 0 0 0 1 0 1
Fulgent Genetics,Fulgent Genetics 0 3 0 0 0 0 1 1
Developmental Genetics Unit,King Faisal Specialist Hospital & Research Centre 0 1 0 1 0 0 0 1
Institute of Human Genetics, Klinikum rechts der Isar 0 1 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 0 0 1 0 0 0 1
UW Hindbrain Malformation Research Program,University of Washington 0 2 0 1 0 0 0 1
CeGaT Praxis fuer Humangenetik Tuebingen 0 0 0 1 0 0 0 1
Centre for Mendelian Genomics,University Medical Centre Ljubljana 0 1 0 0 0 0 1 1
The Molecular Genetic Diagnosis Center, Children’s Hospital of Fudan University 0 0 0 1 0 0 0 1
Department of Pathology and Laboratory Medicine,Sinai Health System 0 0 0 0 0 0 1 1
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 0 0 1 0 0 0 1
Department of Genetics,Sultan Qaboos University Hospital, Oman 0 1 0 0 0 0 1 1
Section for Clinical Neurogenetics,University of Tübingen 0 1 0 0 0 0 1 1

All variants with conflicting interpretations #

Total variants: 36
Download table as spreadsheet
HGVS dbSNP
NM_000151.4(G6PC1):c.247C>T (p.Arg83Cys) rs1801175
NM_000153.4(GALC):c.621G>A (p.Lys207=) rs1428763453
NM_000159.4(GCDH):c.877G>A (p.Ala293Thr) rs121434371
NM_000181.4(GUSB):c.1429C>T (p.Arg477Trp) rs774393243
NM_000282.4(PCCA):c.425G>A (p.Gly142Asp) rs796052019
NM_000317.3(PTS):c.238A>G (p.Met80Val) rs1057517810
NM_000320.3(QDPR):c.344C>T (p.Ser115Leu) rs1407920390
NM_000340.2(SLC2A2):c.1250C>T (p.Pro417Leu) rs121909744
NM_000396.4(CTSK):c.830C>T (p.Ala277Val) rs74315304
NM_000443.4(ABCB4):c.2692G>A (p.Glu898Lys)
NM_001032386.2(SUOX):c.520del (p.Asp174fs) rs1565798380
NM_001040716.2(PC):c.806G>A (p.Arg269Gln) rs1349343839
NM_001080522.2(CC2D2A):c.3084del (p.Lys1029fs) rs386833749
NM_001142279.2(RNASEH2B):c.356A>G (p.Asp119Gly) rs786205483
NM_001146289.1(P3H1):c.570_571del (p.Gly191fs) rs1553143741
NM_001195518.2(MICU1):c.547C>T (p.Gln183Ter) rs777327250
NM_001378615.1(CC2D2A):c.4531T>C (p.Trp1511Arg)
NM_002863.5(PYGL):c.1768+1G>A rs113993982
NM_003193.4(TBCE):c.155_166delGCCACGAAGGGA (p.Ser52_Gly55del) rs767004810
NM_003401.5(XRCC4):c.127T>C (p.Trp43Arg) rs587779351
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_006031.6(PCNT):c.5767C>T (p.Arg1923Ter) rs119479062
NM_006493.4(CLN5):c.448C>T (p.Arg150Ter) rs546989392
NM_007055.4(POLR3A):c.1771-7C>G rs201314157
NM_017890.4(VPS13B):c.1219C>T (p.Gln407Ter) rs386834070
NM_025114.4(CEP290):c.5668G>T (p.Gly1890Ter) rs137852832
NM_025114.4(CEP290):c.5704G>T (p.Glu1902Ter) rs267606719
NM_032504.1(UNC80):c.3793C>T (p.Arg1265Ter) rs864321622
NM_032861.4(SERAC1):c.202C>T (p.Arg68Ter) rs529232938
NM_032861.4(SERAC1):c.442C>T (p.Arg148Ter) rs387907236
NM_033419.5(PGAP3):c.850C>T (p.His284Tyr) rs759541820
NM_058172.6(ANTXR2):c.134T>C (p.Leu45Pro) rs886041401
NM_138422.4(ADAT3):c.430G>A (p.Val144Met) rs730882213
NM_139011.3(HFE):c.77-2168C>G rs1799945

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