ClinVar Miner

Variants from Undiagnosed Diseases Network,NIH with conflicting interpretations

Location: United States — Primary collection method: clinical testing
Minimum review status of the submission from Undiagnosed Diseases Network,NIH: Collection method of the submission from Undiagnosed Diseases Network,NIH:
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
132 54 7 35 4 0 21 61

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
Undiagnosed Diseases Network,NIH pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 7 18 7 0 0
likely pathogenic 17 0 7 1 0
uncertain significance 6 3 0 3 1

Submitter to submitter summary #

Total submitters: 27
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
OMIM 0 45 0 12 0 0 6 18
GeneDx 0 34 0 5 1 0 6 12
GeneReviews 0 2 7 0 0 0 1 8
Ambry Genetics 0 9 0 5 0 0 0 5
Invitae 0 20 0 0 0 0 5 5
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics 0 14 0 4 0 0 1 5
Fulgent Genetics 0 10 0 4 0 0 0 4
CeGaT Praxis fuer Humangenetik Tuebingen 0 1 0 1 0 0 2 3
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine 0 4 0 1 0 0 1 2
Illumina Clinical Services Laboratory,Illumina 0 4 0 0 2 0 0 2
Baylor Miraca Genetics Laboratories, 0 7 0 0 0 0 1 1
Molecular Diagnostics Lab,Nemours Alfred I. duPont Hospital for Children 0 2 0 1 0 0 0 1
Division of Genomic Diagnostics,The Children's Hospital of Philadelphia 0 1 0 1 0 0 0 1
PreventionGenetics 0 0 0 0 1 0 0 1
Counsyl 0 4 0 1 0 0 0 1
Shenzhen Institute of Pediatrics,Shenzhen Children's Hospital 0 0 0 0 0 0 1 1
Whole genome laboratory; Baylor College of Medicine 0 0 0 1 0 0 0 1
CSER_CC_NCGL; University of Washington Medical Center 0 1 0 1 0 0 0 1
Center for Medical Genetics Ghent,University of Ghent 0 0 0 1 0 0 0 1
University of Washington Center for Mendelian Genomics,University of Washington 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
Daryl Scott Lab,Baylor College of Medicine 0 0 0 1 0 0 0 1
SIB Swiss Institute of Bioinformatics 0 0 0 1 0 0 0 1
Rare Disease Group, Clinical Genetics,Karolinska Institutet 0 0 0 0 0 0 1 1
Wong Mito Lab, Molecular and Human Genetics,Baylor College of Medicine 0 2 0 0 1 0 0 1
Diagnostic Laboratory, Department of Genetics,University Medical Center Groningen 0 0 0 1 0 0 0 1
Broad Institute Rare Disease Group,Broad Institute 0 4 0 0 0 0 1 1

All variants with conflicting interpretations #

Total variants: 61
Download table as spreadsheet
HGVS dbSNP
NM_000021.3(PSEN1):c.1141C>T (p.Leu381Phe) rs63750687
NM_000138.4(FBN1):c.871G>T (p.Glu291Ter) rs1232880706
NM_000263.3(NAGLU):c.1834A>G (p.Ser612Gly) rs148881970
NM_000263.3(NAGLU):c.1915G>T (p.Glu639Ter) rs555145190
NM_000264.3(PTCH1):c.395-1G>A rs368869806
NM_000287.3(PEX6):c.273G>A (p.Trp91Ter) rs1010184002
NM_000287.3(PEX6):c.821C>T (p.Pro274Leu) rs61753219
NM_000304.3(PMP22):c.353C>T (p.Thr118Met) rs104894619
NM_000334.4(SCN4A):c.3424C>T (p.Arg1142Ter) rs912001256
NM_000816.3(GABRG2):c.316G>A (p.Ala106Thr) rs796052505
NM_000833.4(GRIN2A):c.2452G>A (p.Ala818Thr) rs1555483699
NM_001005463.2(EBF3):c.488G>A (p.Arg163Gln) rs1057519389
NM_001127222.1(CACNA1A):c.5015G>C (p.Arg1672Pro) rs1057519429
NM_001267578.1(TOR1AIP1):c.554-1G>A rs2245425
NM_001277115.1(DNAH11):c.6727C>T (p.Arg2243Ter) rs201943194
NM_001348768.1(HECW2):c.4334A>G (p.Glu1445Gly) rs878854424
NM_001958.3(EEF1A2):c.796C>T (p.Arg266Trp) rs1555883505
NM_002247.3(KCNMA1):c.2984A>G (p.Asn995Ser) rs886039469
NM_002437.4(MPV17):c.206G>A (p.Trp69Ter) rs267607261
NM_002437.5(MPV17):c.376-9T>G
NM_002693.2(POLG):c.1399G>A (p.Ala467Thr) rs113994095
NM_002693.2(POLG):c.391T>C (p.Tyr131His) rs562847013
NM_002860.3(ALDH18A1):c.755G>A (p.Arg252Gln) rs864321670
NM_003119.2(SPG7):c.1529C>T rs61755320
NM_003156.3(STIM1):c.1588C>T (p.Arg530Cys) rs142239530
NM_003159.2(CDKL5):c.2713+129C>T rs1555955296
NM_003632.2(CNTNAP1):c.1163G>C (p.Arg388Pro) rs779027563
NM_003846.2(PEX11B):c.277C>T (p.Arg93Ter) rs781939614
NM_004004.5(GJB2):c.269T>C (p.Leu90Pro) rs80338945
NM_004895.4(NLRP3):c.2182A>G (p.Ser728Gly) rs147946775
NM_004959.4(NR5A1):c.274C>T (p.Arg92Trp) rs886039769
NM_004992.3(MECP2):c.316C>T (p.Arg106Trp) rs28934907
NM_005186.3(CAPN1):c.1605+5G>A rs375817528
NM_005859.4(PURA):c.299T>C (p.Leu100Pro) rs587782995
NM_006441.3(MTHFS):c.434G>A (p.Arg145Gln) rs753635972
NM_006441.3(MTHFS):c.484C>T (p.Gln162Ter) rs771379232
NM_006662.2(SRCAP):c.7303C>T (p.Arg2435Ter) rs199469465
NM_006767.4(LZTR1):c.1943-256C>T rs761685529
NM_006796.2(AFG3L2):c.2011G>A (p.Gly671Arg) rs151344517
NM_012102.3(RERE):c.4304A>G (p.His1435Arg) rs1553154130
NM_015133.4(MAPK8IP3):c.111C>G (p.Tyr37Ter)
NM_015386.2(COG4):c.1546G>A (p.Gly516Arg) rs1555575860
NM_016011.4(MECR):c.830+2dup rs756421370
NM_016955.3(SEPSECS):c.808dupG (p.Ala270Glyfs) rs776969714
NM_018116.3(MSTO1):c.971C>T (p.Thr324Ile) rs622288
NM_020320.3(RARS2):c.419T>G (p.Phe140Cys) rs772887102
NM_021911.2(GABRB2):c.904G>A (p.Val302Met) rs1085307993
NM_024496.3(IRF2BPL):c.519C>G (p.Tyr173Ter) rs1555377415
NM_024496.3(IRF2BPL):c.562C>T (p.Arg188Ter) rs1345176461
NM_024818.4(UBA5):c.562C>T (p.Arg188Ter) rs374052333
NM_025137.3(SPG11):c.642delT (p.Phe214Leufs) rs312262717
NM_052876.3(NACC1):c.892C>T (p.Arg298Trp) rs1060505041
NM_144991.2(TSPEAR):c.589C>T (p.Arg197Ter) rs139455627
NM_145207.2(SPATA5):c.983_985delCAA (p.Thr330del) rs796052243
NM_152296.3(ATP1A3):c.2767G>A (p.Asp923Asn) rs267606670
NM_152419.2(HGSNAT):c.1267G>T (p.Gly423Trp) rs1064795522
NM_153033.4(KCTD7):c.280C>T (p.Arg94Trp) rs387907260
NM_153033.4(KCTD7):c.456G>A (p.Val152=) rs796052686
NM_172079.2(CAMK2B):c.416C>T (p.Pro139Leu) rs1554389088
NM_199165.2(ADSSL1):c.910G>A (p.Asp304Asn) rs140614802
NR_023343.1(RNU4ATAC):n.48G>A rs863225422

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