ClinVar Miner

Variants from Suna and Inan Kirac Foundation Neurodegeneration Research Laboratory, Koc University with conflicting interpretations

Location: Turkey  Primary collection method: research
Minimum review status of the submission from Suna and Inan Kirac Foundation Neurodegeneration Research Laboratory, Koc University: Collection method of the submission from Suna and Inan Kirac Foundation Neurodegeneration Research Laboratory, Koc University:
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
148 23 0 21 4 0 7 29

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
Suna and Inan Kirac Foundation Neurodegeneration Research Laboratory, Koc University pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 3 1 0 0
likely pathogenic 18 0 3 0 0
uncertain significance 2 1 0 1 1
likely benign 1 0 2 0 0

Submitter to submitter summary #

Total submitters: 18
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
OMIM 0 5 0 10 0 0 2 12
Invitae 0 10 0 7 1 0 4 12
Illumina Laboratory Services, Illumina 0 1 0 1 1 0 1 3
Revvity Omics, Revvity 0 1 0 1 0 0 1 2
MGZ Medical Genetics Center 0 0 0 1 0 0 1 2
Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München 0 0 0 2 0 0 0 2
CeGaT Center for Human Genetics Tuebingen 0 1 0 0 1 0 1 2
GeneDx 0 2 0 1 0 0 0 1
Institute of Human Genetics, Cologne University 0 1 0 1 0 0 0 1
Mendelics 0 0 0 1 0 0 0 1
Mayo Clinic Laboratories, Mayo Clinic 0 0 0 0 1 0 0 1
SIB Swiss Institute of Bioinformatics 0 0 0 1 0 0 0 1
Reproductive Health Research and Development, BGI Genomics 0 0 0 0 0 0 1 1
Genome-Nilou Lab 0 2 0 1 0 0 0 1
3billion 0 2 0 1 0 0 0 1
Neuberg Centre For Genomic Medicine, NCGM 0 0 0 1 0 0 0 1
Human Genetics Bochum, Ruhr University Bochum 0 0 0 1 0 0 0 1
Inherited Neuropathy Consortium Ii, University Of Miami 0 0 0 0 1 0 0 1

All variants with conflicting interpretations #

Total variants: 29
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000454.5(SOD1):c.272A>C (p.Asp91Ala) rs80265967 0.00126
NM_014845.6(FIG4):c.122T>C (p.Ile41Thr) rs121908287 0.00117
NM_001097577.3(ANG):c.208A>G (p.Ile70Val) rs121909541 0.00073
NM_014845.6(FIG4):c.1940A>G (p.Tyr647Cys) rs150301327 0.00008
NM_004320.6(ATP2A1):c.428G>A (p.Arg143Gln) rs750195772 0.00005
NM_013444.4(UBQLN2):c.1573C>T (p.Pro525Ser) rs369947678 0.00005
NM_007375.4(TARDBP):c.1144G>A (p.Ala382Thr) rs367543041 0.00003
NM_007375.4(TARDBP):c.1147A>G (p.Ile383Val) rs80356740 0.00003
NM_031448.6(C19orf12):c.-2C>T rs397514477 0.00003
NM_015046.7(SETX):c.5825T>C (p.Ile1942Thr) rs773379832 0.00001
NM_021625.5(TRPV4):c.943C>T (p.Arg315Trp) rs267607143 0.00001
NM_000021.4(PSEN1):c.698T>C (p.Met233Thr) rs63751024
NM_000311.5(PRNP):c.392G>T (p.Gly131Val) rs74315410
NM_000454.5(SOD1):c.122A>G (p.Glu41Gly) rs1568809149
NM_000454.5(SOD1):c.352C>G (p.Leu118Val) rs199474723
NM_000454.5(SOD1):c.43G>A (p.Val15Met) rs1568807400
NM_000454.5(SOD1):c.446T>G (p.Val149Gly) rs1476760624
NM_000454.5(SOD1):c.68A>T (p.Gln23Leu) rs1169198442
NM_001008212.2(OPTN):c.1078_1079del (p.Lys360fs) rs1833438306
NM_002180.3(IGHMBP2):c.638A>G (p.His213Arg) rs137852666
NM_003119.4(SPG7):c.1324+2T>G rs1597635592
NM_004960.4(FUS):c.1562G>T (p.Arg521Leu) rs121909671
NM_006070.6(TFG):c.854C>T (p.Pro285Leu) rs207482230
NM_006736.6(DNAJB2):c.14A>G (p.Tyr5Cys) rs730882140
NM_007375.4(TARDBP):c.1042G>T (p.Gly348Cys) rs80356733
NM_007375.4(TARDBP):c.893G>T (p.Gly298Val) rs1643653768
NM_013254.4(TBK1):c.1436_1437del (p.Val479fs) rs876657405
NM_025137.4(SPG11):c.7155T>G (p.Tyr2385Ter) rs778305085
NM_213720.3(CHCHD10):c.176C>T (p.Ser59Leu) rs587777574

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