ClinVar Miner

Variants from Bioinformatics Core,Luxembourg Center for Systems Biomedicine with conflicting interpretations

Location: Luxembourg — Primary collection method: case-control
Minimum review status of the submission from Bioinformatics Core,Luxembourg Center for Systems Biomedicine: Collection method of the submission from Bioinformatics Core,Luxembourg Center for Systems Biomedicine:
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 Variants with at least 2 submissions 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 kind of conflict
50 4 0 1 0 0 57 57

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
Bioinformatics Core,Luxembourg Center for Systems Biomedicine likely pathogenic uncertain significance likely benign benign
pathogenic 1 47 26 14

Submitter to submitter summary #

Total submitters: 22
Download table as spreadsheet
Submitter Variants with only 1 submission Variants with at least 2 submissions 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 kind of conflict
Invitae 0 1 0 0 0 0 41 41
GeneDx 0 1 0 0 0 0 29 29
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics 0 1 0 0 0 0 22 22
Ambry Genetics 0 1 0 0 0 0 19 19
Genetic Services Laboratory, University of Chicago 0 0 0 0 0 0 17 17
Athena Diagnostics Inc 0 0 0 0 0 0 15 15
Illumina Clinical Services Laboratory,Illumina 0 1 0 0 0 0 15 15
Fulgent Genetics 0 0 0 0 0 0 6 6
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics 0 0 0 0 0 0 6 6
CeGaT Praxis fuer Humangenetik Tuebingen 0 0 0 1 0 0 4 5
GeneReviews 0 4 0 0 0 0 4 4
Diagnostic Laboratory, Department of Genetics,University Medical Center Groningen 0 0 0 0 0 0 3 3
Claritas Genomics 0 0 0 0 0 0 2 2
PreventionGenetics 0 0 0 0 0 0 2 2
Center for Human Genetics, Inc 0 0 0 0 0 0 1 1
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine 0 0 0 0 0 0 1 1
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories 0 0 0 0 0 0 1 1
UniProtKB/Swiss-Prot 0 1 0 0 0 0 1 1
Centre for Mendelian Genomics,University Medical Centre Ljubljana 0 1 0 0 0 0 1 1
SIB Swiss Institute of Bioinformatics 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 0 0 1 1
Institute for Genomic Medicine (IGM) Clinical Laboratory,Nationwide Children's Hospital 0 0 0 0 0 0 1 1

All variants with conflicting interpretations #

Total variants: 57
Download table as spreadsheet
HGVS dbSNP
NM_000833.4(GRIN2A):c.2441T>C (p.Ile814Thr) rs780654733
NM_000833.4(GRIN2A):c.547T>A (p.Phe183Ile) rs587780353
NM_001130438.2(SPTAN1):c.1303T>G (p.Ser435Ala) rs144787939
NM_001130438.2(SPTAN1):c.3673C>T (p.Arg1225Trp) rs569997507
NM_001130438.2(SPTAN1):c.3720-5T>G rs200543425
NM_001130438.2(SPTAN1):c.4283C>G (p.Ala1428Gly) rs143166100
NM_001184880.1(PCDH19):c.3319C>G (p.Arg1107Gly) rs191333060
NM_001199107.1(TBC1D24):c.169C>T (p.Arg57Cys) rs202162520
NM_001242896.1(DEPDC5):c.2020C>T (p.Arg674Cys) rs181347577
NM_001242896.1(DEPDC5):c.2135C>T (p.Ser712Phe) rs16989535
NM_001242896.1(DEPDC5):c.3265-3C>T rs371377906
NM_001242896.2(DEPDC5):c.268G>A (p.Val90Ile) rs768456731
NM_001242896.2(DEPDC5):c.3241A>C (p.Thr1081Pro) rs142540948
NM_001242896.2(DEPDC5):c.3484A>G (p.Ser1162Gly) rs886039280
NM_001242896.2(DEPDC5):c.814G>T (p.Val272Leu) rs187334123
NM_001271.3(CHD2):c.4058C>T (p.Pro1353Leu) rs755088564
NM_001271.3(CHD2):c.4534C>T (p.Arg1512Trp) rs755898320
NM_001308117.1(RBFOX1):c.1186G>A (p.Gly396Ser) rs145873257
NM_002977.3(SCN9A):c.1846G>A (p.Gly616Arg) rs201338643
NM_002977.3(SCN9A):c.1946C>T (p.Thr649Met) rs200965749
NM_002977.3(SCN9A):c.2969A>G (p.Tyr990Cys) rs199692186
NM_002977.3(SCN9A):c.3316G>T (p.Val1106Leu) rs200817435
NM_002977.3(SCN9A):c.3799C>G (p.Leu1267Val) rs180922748
NM_004315.5(ASAH1):c.668A>T (p.Tyr223Phe) rs150268016
NM_004315.5(ASAH1):c.677T>C (p.Met226Thr) rs141068211
NM_004519.3(KCNQ3):c.1885G>C (p.Val629Leu) rs185511111
NM_004519.3(KCNQ3):c.2263G>A (p.Asp755Asn) rs150821246
NM_005045.3(RELN):c.10093G>A (p.Val3365Ile) rs115035120
NM_005045.3(RELN):c.139G>A (p.Glu47Lys) rs139648092
NM_005045.3(RELN):c.2932A>G (p.Thr978Ala) rs3025962
NM_005045.3(RELN):c.3477C>A (p.Asn1159Lys) rs114684479
NM_005045.3(RELN):c.5284G>A (p.Val1762Ile) rs79499902
NM_005045.3(RELN):c.8843+3A>C rs200124755
NM_005506.3(SCARB2):c.1010T>C (p.Met337Thr) rs147324129
NM_005506.3(SCARB2):c.80G>A (p.Arg27Gln) rs368906199
NM_006920.4(SCN1A):c.1625G>A (p.Arg542Gln) rs121918817
NM_006920.4(SCN1A):c.3488C>G (p.Thr1163Ser) rs121918799
NM_014141.5(CNTNAP2):c.1249G>T (p.Asp417Tyr) rs147815978
NM_014141.5(CNTNAP2):c.2147A>G (p.Tyr716Cys) rs760930032
NM_014141.5(CNTNAP2):c.2290C>A (p.His764Asn) rs201446615
NM_014141.5(CNTNAP2):c.2651G>A (p.Arg884Gln) rs758630057
NM_014141.5(CNTNAP2):c.3577G>A (p.Ala1193Thr) rs751491210
NM_014141.5(CNTNAP2):c.755-5C>T rs369675346
NM_015284.3(SZT2):c.5344C>T (p.Arg1782Cys) rs147748994
NM_016373.3(WWOX):c.754C>G (p.Pro252Ala) rs75559202
NM_016373.3(WWOX):c.990C>G (p.Asn330Lys) rs117209694
NM_020361.4(CPA6):c.557A>G (p.Lys186Arg) rs199576384
NM_020361.4(CPA6):c.619C>G (p.Gln207Glu) rs35993949
NM_020361.4(CPA6):c.799G>A (p.Gly267Arg) rs61738009
NM_020822.2(KCNT1):c.3641G>A (p.Arg1214Gln) rs138282349
NM_021007.2(SCN2A):c.3457G>A (p.Glu1153Lys) rs200138205
NM_145891.2(RBFOX1):c.737-5C>T rs147023054
NM_153026.2(PRICKLE1):c.100G>A (p.Ala34Thr) rs781255236
NM_153026.2(PRICKLE1):c.2216C>T (p.Ser739Phe) rs138452760
NM_153026.2(PRICKLE1):c.370G>A (p.Ala124Thr) rs79087668
NM_198859.3(PRICKLE2):c.1314G>C (p.Gln438His) rs202170644
NM_198903.2(GABRG2):c.549-3T>G rs750459631

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