ClinVar Miner

Variants from Intergen, Intergen Genetics and Rare Diseases Diagnosis Center with conflicting interpretations

Location: Turkey  Primary collection method: clinical testing
Minimum review status of the submission from Intergen, Intergen Genetics and Rare Diseases Diagnosis Center: Collection method of the submission from Intergen, Intergen Genetics and Rare Diseases Diagnosis Center:
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
102 31 0 31 1 1 7 38

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
Intergen, Intergen Genetics and Rare Diseases Diagnosis Center pathogenic likely pathogenic uncertain significance association likely risk allele risk factor
pathogenic 0 25 4 0 0 0
likely pathogenic 6 0 0 0 0 0
uncertain significance 1 2 0 0 0 0
likely benign 1 0 1 0 0 0
established risk allele 1 1 1 1 1 1

Submitter to submitter summary #

Total submitters: 38
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 8 0 4 0 0 3 7
Counsyl 0 6 0 6 0 0 0 6
OMIM 0 17 0 4 0 0 1 5
Invitae 0 27 0 3 1 1 0 5
Centre for Mendelian Genomics, University Medical Centre Ljubljana 0 2 0 3 0 1 0 4
Institute of Human Genetics, University of Leipzig Medical Center 0 4 0 4 0 0 0 4
Mendelics 0 7 0 0 0 1 2 3
Fulgent Genetics, Fulgent Genetics 0 8 0 3 0 0 0 3
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology 0 1 0 2 0 0 1 3
3billion 0 5 0 3 0 0 0 3
Baylor Genetics 0 15 0 1 0 1 0 2
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 6 0 1 0 1 0 2
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 13 0 1 0 1 0 2
Natera, Inc. 0 5 0 2 0 0 0 2
Neuberg Centre For Genomic Medicine, NCGM 0 5 0 1 0 1 0 2
Center for Human Genetics, Inc, Center for Human Genetics, Inc 0 1 0 0 0 1 0 1
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 0 2 0 1 0 0 0 1
Ambry Genetics 0 0 0 0 0 1 0 1
Revvity Omics, Revvity 0 7 0 1 0 0 0 1
Sema4, Sema4 0 0 0 0 0 1 0 1
Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine 0 0 0 1 0 0 0 1
Illumina Laboratory Services, Illumina 0 7 0 0 0 1 0 1
UCLA Clinical Genomics Center, UCLA 0 0 0 1 0 0 0 1
Hadassah Hebrew University Medical Center 0 1 0 1 0 0 0 1
Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center 0 0 0 1 0 0 0 1
Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India 0 0 0 1 0 0 0 1
Undiagnosed Diseases Network, NIH 0 1 0 0 0 1 0 1
Genetics and Molecular Pathology, SA Pathology 0 3 0 1 0 0 0 1
Human Genomics Unit, Institute for molecular medicine Finland (FIMM) 0 0 0 1 0 0 0 1
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 0 0 1 0 0 0 1
Department Of Genetics, Sultan Qaboos University Hospital, Sultan Qaboos University 0 1 0 0 0 0 1 1
Al Jalila Children's Genomics Center, Al Jalila Childrens Speciality Hospital 0 1 0 0 0 0 1 1
Zotz-Klimas Genetics Lab, MVZ Zotz Klimas 0 4 0 0 0 1 0 1
Molecular Biology Laboratory, Fundació Puigvert 0 0 0 1 0 0 0 1
Eurofins-Biomnis 0 0 0 0 0 1 0 1
Clinical Laboratory Sciences Program (CLSP), King Saud bin Abdulaziz University for Health Sciences (KSAU-HS) 0 3 0 1 0 0 0 1
KCCC/NGS Laboratory, Kuwait Cancer Control Center 0 1 0 0 0 1 0 1
ClinGen Severe Combined Immunodeficiency Variant Curation Expert Panel, ClinGen 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 38
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_001379610.1(SPINK1):c.101A>G (p.Asn34Ser) rs17107315 0.00797
NM_000500.9(CYP21A2):c.1360C>T (p.Pro454Ser) rs6445 0.00530
NM_001048174.2(MUTYH):c.1103G>A (p.Gly368Asp) rs36053993 0.00341
NM_000350.3(ABCA4):c.5882G>A (p.Gly1961Glu) rs1800553 0.00269
NM_000065.5(C6):c.2381+2T>C rs76202909 0.00242
NM_000431.4(MVK):c.1129G>A (p.Val377Ile) rs28934897 0.00156
NM_000243.3(MEFV):c.2177T>C (p.Val726Ala) rs28940579 0.00147
NM_001386094.1(AGBL1):c.3044G>C (p.Cys1015Ser) rs181958589 0.00124
NM_005357.4(LIPE):c.551C>A (p.Ser184Ter) rs149927060 0.00083
NM_022835.3(PLEKHG2):c.610C>T (p.Arg204Trp) rs201201843 0.00039
NM_000402.4(G6PD):c.653C>T (p.Ser218Phe) rs5030868 0.00028
NM_004562.3(PRKN):c.719C>T (p.Thr240Met) rs137853054 0.00016
NM_016327.3(UPB1):c.105-2A>G rs138081800 0.00010
NM_000341.4(SLC3A1):c.647C>T (p.Thr216Met) rs369641941 0.00009
NM_000243.3(MEFV):c.1958G>A (p.Arg653His) rs104895085 0.00007
NM_000341.4(SLC3A1):c.1354C>T (p.Arg452Trp) rs201502095 0.00007
NM_000402.4(G6PD):c.1039G>A (p.Glu347Lys) rs137852339 0.00004
NM_153766.3(KCNJ1):c.601C>T (p.Leu201Phe) rs200320892 0.00004
NM_000402.4(G6PD):c.1093G>A (p.Ala365Thr) rs5030869 0.00003
NM_000536.4(RAG2):c.217C>T (p.Arg73Cys) rs193922574 0.00003
NM_001083116.3(PRF1):c.1122G>A (p.Trp374Ter) rs104894176 0.00003
NM_002435.3(MPI):c.1193T>C (p.Ile398Thr) rs369326210 0.00003
NM_000532.5(PCCB):c.1304A>G (p.Tyr435Cys) rs121964961 0.00002
NM_000085.5(CLCNKB):c.937_940dup (p.Arg314delinsLysTer) rs779593707 0.00001
NM_000199.5(SGSH):c.571G>A (p.Gly191Arg) rs753666460 0.00001
NM_000478.6(ALPL):c.542C>T (p.Ser181Leu) rs199590449 0.00001
NM_001048174.2(MUTYH):c.800C>T (p.Pro267Leu) rs374950566 0.00001
NM_006424.3(SLC34A2):c.316G>C (p.Gly106Arg) rs137853142 0.00001
NM_000235.4(LIPA):c.694G>T (p.Glu232Ter)
NM_000277.3(PAH):c.1054G>T (p.Gly352Cys) rs62508686
NM_000466.3(PEX1):c.1108del (p.Ile370fs) rs61750406
NM_000587.4(C7):c.1561C>A (p.Arg521Ser) rs121964920
NM_001807.6(CEL):c.337C>T (p.Gln113Ter) rs1200339761
NM_006922.4(SCN3A):c.2624T>C (p.Ile875Thr) rs1057518801
NM_014334.4(FRRS1L):c.260C>G (p.Pro87Arg) rs768169514
NM_018245.3(OGDHL):c.895A>G (p.Arg299Gly) rs924975413
NM_020975.6(RET):c.1858T>C (p.Cys620Arg) rs77316810
NM_022915.5(MRPL44):c.233G>A (p.Arg78Gln) rs761343107

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