ClinVar Miner

Variants from Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan with conflicting interpretations

Location: Argentina  Primary collection method: clinical testing
Minimum review status of the submission from Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan: Collection method of the submission from Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan:
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
995 1309 0 58 16 10 7 88

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
Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan pathogenic likely pathogenic uncertain significance likely benign benign association drug response protective risk factor uncertain risk allele
pathogenic 0 3 1 0 0 0 0 0 0 0
likely pathogenic 0 0 4 0 0 0 0 0 0 0
uncertain significance 1 0 0 1 1 0 0 0 0 0
benign 0 1 15 55 0 3 1 3 2 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
Genetic Services Laboratory, University of Chicago 0 8 0 19 0 0 0 19
GeneDx 0 1115 0 9 0 0 1 10
Department of Pathology and Laboratory Medicine, Sinai Health System 0 4 0 0 10 0 0 10
Invitae 0 207 0 5 1 0 3 9
Genome Diagnostics Laboratory, University Medical Center Utrecht 0 71 0 8 0 0 0 8
OMIM 0 5 0 0 1 6 0 7
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 24 0 6 0 0 0 6
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) 0 4 0 6 0 0 0 6
HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas 0 0 0 0 4 2 0 6
Illumina Laboratory Services, Illumina 0 15 0 1 1 0 0 2
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital 0 7 0 2 0 0 0 2
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 306 0 1 0 0 0 1
Ambry Genetics 0 2 0 0 0 0 1 1
Revvity Omics, Revvity 0 0 0 0 0 0 1 1
Clinical Genetics, Academic Medical Center 0 52 0 1 0 0 0 1
Mendelics 0 2 0 0 1 0 0 1
Mayo Clinic Laboratories, Mayo Clinic 0 20 0 1 0 0 0 1
Genomic Research Center, Shahid Beheshti University of Medical Sciences 0 0 0 1 0 0 0 1
Database of Curated Mutations (DoCM) 0 0 0 1 0 0 0 1
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ 0 91 0 1 0 0 0 1
Genome Diagnostics Laboratory, Amsterdam University Medical Center 0 10 0 1 0 0 0 1
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 51 0 1 0 0 0 1
Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute 0 29 0 1 0 0 0 1
St. Jude Molecular Pathology, St. Jude Children's Research Hospital 0 1 0 0 0 0 1 1
Institute of Clinical Molecular Biology, Kiel University 0 0 0 0 0 0 1 1
Bioinformatics Institute, Agency for Science, Technology and Research 0 0 0 0 0 1 0 1
Centro Dermatológico Federico Lleras Acosta, Hospital Universitario Centro Dermatológico Federico Lleras Acosta 0 0 0 0 0 1 0 1

All variants with conflicting interpretations #

Total variants: 88
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_025099.6(CTC1):c.2458A>G (p.Ile820Val) rs3027238 0.94552
NM_018344.6(SLC29A3):c.383+8A>G rs2243540 0.87959
NM_018344.6(SLC29A3):c.976A>G (p.Ile326Val) rs2487068 0.87306
NM_018344.6(SLC29A3):c.714T>C (p.Thr238=) rs2252997 0.87276
NM_018344.6(SLC29A3):c.715G>A (p.Val239Ile) rs2252996 0.84751
NM_018344.6(SLC29A3):c.1008T>C (p.Gly336=) rs1084004 0.84205
NM_025099.6(CTC1):c.3013A>G (p.Ile1005Val) rs3826543 0.77529
NM_000179.3(MSH6):c.3802-40C>G rs3136367 0.73398
NM_002185.5(IL7R):c.197T>C (p.Ile66Thr) rs1494558 0.68368
NM_000101.4(CYBA):c.214T>C (p.Tyr72His) rs4673 0.64973
NM_018344.6(SLC29A3):c.473C>T (p.Ser158Phe) rs780668 0.61569
NM_000243.3(MEFV):c.942C>T (p.Arg314=) rs224213 0.61317
NM_000660.7(TGFB1):c.29C>T (p.Pro10Leu) rs1800470 0.60129
NM_016816.4(OAS1):c.1039-1G>A rs10774671 0.59385
NM_003331.5(TYK2):c.1669+7T>C rs280519 0.52527
NM_000383.4(AIRE):c.1578T>C (p.Asp526=) rs1133779 0.49415
NM_000243.3(MEFV):c.306T>C (p.Asp102=) rs224225 0.48544
NM_000243.3(MEFV):c.495C>A (p.Ala165=) rs224223 0.48450
NM_000448.3(RAG1):c.746A>G (p.His249Arg) rs3740955 0.48211
NM_016816.4(OAS1):c.484G>A (p.Gly162Ser) rs1131454 0.47874
NM_018344.6(SLC29A3):c.52A>G (p.Arg18Gly) rs2277257 0.47837
NM_199242.3(UNC13D):c.2599A>G (p.Lys867Glu) rs1135688 0.47045
NM_000416.3(IFNGR1):c.-56T>C rs2234711 0.42896
NM_000243.3(MEFV):c.1764G>A (p.Pro588=) rs1231122 0.41230
NM_001065.4(TNFRSF1A):c.36A>G (p.Pro12=) rs767455 0.39963
NM_000383.4(AIRE):c.1197T>C (p.Ala399=) rs1800521 0.39834
NM_000243.3(MEFV):c.1760-30T>A rs1231123 0.39404
NM_001167.4(XIAP):c.1268A>C (p.Gln423Pro) rs5956583 0.38953
NM_001065.4(TNFRSF1A):c.625+10A>G rs1800693 0.38055
NM_000569.8(FCGR3A):c.526T>G (p.Phe176Val) rs396991 0.32987
NM_000565.4(IL6R):c.1073A>C (p.Asp358Ala) rs2228145 0.31732
NM_181523.3(PIK3R1):c.334+14A>C rs706714 0.31124
NM_181523.3(PIK3R1):c.219C>T (p.Tyr73=) rs706713 0.31073
NM_000074.3(CD40LG):c.410-13T>C rs3092923 0.27747
NM_153218.4(LACC1):c.760A>G (p.Ile254Val) rs3764147 0.26736
NM_181523.3(PIK3R1):c.978G>A (p.Met326Ile) rs3730089 0.22679
NM_000383.4(AIRE):c.681C>T (p.Gly227=) rs1055311 0.21613
NM_000243.3(MEFV):c.605G>A (p.Arg202Gln) rs224222 0.20976
NM_006384.4(CIB1):c.87-84C>T rs4451921 0.20932
NM_000270.4(PNP):c.151G>A (p.Gly51Ser) rs1049564 0.20682
NM_080424.4(SP110):c.617C>T (p.Ala206Val) rs28930679 0.20608
NM_000383.4(AIRE):c.588C>T (p.Ser196=) rs878081 0.18544
NM_000431.4(MVK):c.510C>T (p.Asp170=) rs2287218 0.17165
NM_206937.2(LIG4):c.26C>T (p.Thr9Ile) rs1805388 0.16468
NM_018648.3(NOP10):c.-95T>C rs2169480 0.13873
NM_006904.7(PRKDC):c.10301T>C (p.Ile3434Thr) rs7830743 0.13382
NM_000179.3(MSH6):c.260+22C>G rs55927047 0.13136
NM_001318777.2(TIRAP):c.539C>T (p.Ser180Leu) rs8177374 0.10979
NM_001141945.3(ACTA2):c.-24+1440C>T rs2234767 0.10602
NM_001289125.3(IFNAR2):c.23T>C (p.Phe8Ser) rs2229207 0.08893
NM_003721.4(RFXANK):c.144G>C (p.Glu48Asp) rs34282046 0.04400
NM_022168.4(IFIH1):c.2808-75G>T rs3761652 0.03297
NM_022168.4(IFIH1):c.1524+90G>A rs16846555 0.03287
NM_006904.7(PRKDC):c.6346-105A>G rs8178148 0.01827
NM_000321.3(RB1):c.929G>A (p.Gly310Glu) rs200844292 0.00029
NM_001037.5(SCN1B):c.265C>T (p.Arg89Cys) rs766910280 0.00004
NM_001371596.2(MFSD8):c.864-1G>A rs571950296 0.00002
NM_000051.4(ATM):c.1236-3del rs34325032
NM_000051.4(ATM):c.1236-3dup rs34325032
NM_000051.4(ATM):c.2922-8del rs373881770
NM_000051.4(ATM):c.3403-13dup rs3218681
NM_000051.4(ATM):c.6573-42del rs11366542
NM_000051.4(ATM):c.6573-43_6573-42del rs11366542
NM_000081.4(LYST):c.11268-5del rs36014994
NM_000179.3(MSH6):c.3557-4del rs267608102
NM_000179.3(MSH6):c.3646+35_3646+38del rs1805181
NM_000179.3(MSH6):c.4002-10del rs59056100
NM_000243.3(MEFV):c.414A>G (p.Gly138=) rs224224
NM_000314.8(PTEN):c.-511G>A rs12573787
NM_000314.8(PTEN):c.802-3dup rs34003473
NM_000321.3(RB1):c.1215+1G>A rs587776783
NM_000321.3(RB1):c.1735C>T (p.Arg579Ter) rs121913305
NM_000321.3(RB1):c.1961T>A (p.Val654Glu) rs769113950
NM_000321.3(RB1):c.1964A>G (p.Tyr655Cys) rs774196937
NM_000383.4(AIRE):c.834C>G (p.Ser278Arg) rs1800520
NM_001128148.3(TFRC):c.1678-5_1678-4inv
NM_001165963.4(SCN1A):c.4036T>C (p.Ser1346Pro) rs1553525337
NM_001197104.2(KMT2A):c.5961+37del rs57102960
NM_001261826.3(AP3D1):c.593-18_593-17delinsCG rs374386030
NM_001289125.3(IFNAR2):c.28T>G (p.Phe10Val) rs1051393
NM_001289125.3(IFNAR2):c.541-50A>G
NM_001289125.3(IFNAR2):c.98-43T>C
NM_001291415.2(KDM6A):c.2859-5del rs10605935
NM_001372051.1(CASP8):c.595+133del rs397826156
NM_003560.4(PLA2G6):c.1797C>G (p.Phe599Leu) rs1555979298
NM_007327.4(GRIN1):c.2530C>T (p.Arg844Cys) rs1554770667
NM_022168.4(IFIH1):c.1095+98_1095+102del rs141134657
NM_139276.3(STAT3):c.468+58del rs397712608

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