ClinVar Miner

Variants from Clinical Genomics Lab,St. Jude Children's Research Hospital with conflicting interpretations

Location: United States — Primary collection method: clinical testing
Minimum review status of the submission from Clinical Genomics Lab,St. Jude Children's Research Hospital: Collection method of the submission from Clinical Genomics Lab,St. Jude Children's Research Hospital:
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
41 94 5 14 68 2 13 92

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
Clinical Genomics Lab,St. Jude Children's Research Hospital pathogenic likely pathogenic uncertain significance likely benign benign risk factor other
pathogenic 0 9 3 2 0 1 0
likely pathogenic 5 0 4 0 0 0 0
uncertain significance 3 3 5 62 27 0 1

Submitter to submitter summary #

Total submitters: 42
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 0 112 0 2 45 0 4 51
Ambry Genetics 0 100 0 1 29 0 3 33
GeneDx 0 56 0 3 21 0 3 27
Color 0 48 0 1 21 0 1 23
Integrated Genetics/Laboratory Corporation of America 0 32 0 1 17 0 0 18
Sharing Clinical Reports Project (SCRP) 0 3 0 0 9 0 0 9
Quest Diagnostics Nichols Institute San Juan Capistrano 0 18 0 1 7 0 0 8
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine 0 16 0 3 3 0 1 7
Illumina Clinical Services Laboratory,Illumina 0 7 0 1 6 0 0 7
OMIM 0 12 0 3 0 1 2 6
Mendelics 0 18 0 2 4 0 0 6
Counsyl 0 39 0 2 2 0 1 5
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics 0 10 0 0 5 0 0 5
Database of Curated Mutations (DoCM) 0 0 0 3 0 0 2 5
Biesecker Lab/Clinical Genomics Section,National Institutes of Health 0 0 4 0 0 0 0 4
PreventionGenetics,PreventionGenetics 0 13 0 0 4 0 0 4
CSER _CC_NCGL, University of Washington 0 4 0 1 1 0 2 4
ClinGen RASopathy Variant Curation Expert Panel 0 1 0 0 4 0 0 4
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 0 10 0 1 2 0 0 3
Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) 0 1 0 0 2 0 0 2
Vantari Genetics 0 0 0 1 1 0 0 2
True Health Diagnostics 0 5 0 0 2 0 0 2
German Consortium for Hereditary Breast and Ovarian Cancer Center Cologne,University Hospital Cologne 0 1 0 1 0 0 1 2
Center for Human Genetics, Inc 0 3 0 0 1 0 0 1
Genetic Services Laboratory, University of Chicago 0 4 0 0 1 0 0 1
Division of Genomic Diagnostics,The Children's Hospital of Philadelphia 0 4 0 0 0 0 1 1
GeneReviews 0 3 0 1 0 0 0 1
Mayo Clinic Genetic Testing Laboratories,Mayo Clinic 0 9 0 0 1 0 0 1
Fulgent Genetics,Fulgent Genetics 0 10 0 1 0 0 0 1
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) 0 0 0 1 0 0 0 1
Science for Life laboratory, Karolinska Institutet 0 0 1 0 0 0 0 1
Systems Biology Platform Zhejiang California International NanoSystems Institute 0 0 0 0 0 1 0 1
Human Genome Sequencing Center Clinical Lab,Baylor College of Medicine 0 1 0 1 0 0 0 1
Section on Endocrinology and Genetics,National Institutes of Health / The Eunice Kennedy Shriver National Institute of Child Health and Human Development 0 0 0 1 0 0 0 1
GeneKor MSA 0 3 0 1 0 0 0 1
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics 0 0 0 0 1 0 0 1
Cancer Genetics Laboratory,Peter MacCallum Cancer Centre 0 0 0 0 1 0 0 1
CeGaT Praxis fuer Humangenetik Tuebingen 0 3 0 0 1 0 0 1
Yale Center for Mendelian Genomics,Yale University 0 0 0 1 0 0 0 1
Laboratory of Molecular Neuropathology,The University of Texas Health Science Center at Houston 0 0 0 0 0 0 1 1
Gharavi Laboratory,Columbia University 0 0 0 0 1 0 0 1
ClinGen CDH1 Variant Curation Expert Panel 0 0 0 0 1 0 0 1

All variants with conflicting interpretations #

Total variants: 92
Download table as spreadsheet
HGVS dbSNP
NM_000038.6(APC):c.1240C>T (p.Arg414Cys) rs137854567
NM_000038.6(APC):c.2476T>G (p.Leu826Val) rs145245264
NM_000038.6(APC):c.6679G>T (p.Gly2227Cys) rs367905430
NM_000038.6(APC):c.7109G>T (p.Gly2370Val) rs140079759
NM_000038.6(APC):c.7513C>G (p.Arg2505Gly) rs79630786
NM_000051.3(ATM):c.8786+1G>A rs17174393
NM_000059.3(BRCA2):c.1909+9_1909+10del rs527732001
NM_000059.3(BRCA2):c.232C>T (p.Pro78Ser) rs398122745
NM_000059.3(BRCA2):c.3916G>A (p.Val1306Ile) rs80358636
NM_000059.3(BRCA2):c.4474_4477AAAG[1] (p.Glu1493fs) rs80359454
NM_000059.3(BRCA2):c.4850G>A (p.Ser1617Asn) rs397507341
NM_000059.3(BRCA2):c.5896C>T (p.His1966Tyr) rs80358822
NM_000059.3(BRCA2):c.6560C>T (p.Pro2187Leu) rs56019712
NM_000059.3(BRCA2):c.8918G>A (p.Arg2973His) rs80359143
NM_000059.3(BRCA2):c.8972G>A (p.Arg2991His) rs80359150
NM_000059.3(BRCA2):c.9433G>C (p.Val3145Leu) rs587776476
NM_000075.4(CDK4):c.625C>T (p.Arg209Cys) rs140644696
NM_000075.4(CDK4):c.776C>T (p.Ser259Leu) rs201617914
NM_000077.4(CDKN2A):c.146T>C (p.Ile49Thr) rs199907548
NM_000179.2(MSH6):c.3961A>G (p.Arg1321Gly) rs41295278
NM_000179.2(MSH6):c.643G>A (p.Val215Ile) rs145959653
NM_000179.2(MSH6):c.942C>G (p.Ser314Arg) rs150440246
NM_000251.2(MSH2):c.1360A>G (p.Ile454Val) rs587781627
NM_000251.2(MSH2):c.2120G>A (p.Cys707Tyr) rs373226409
NM_000251.2(MSH2):c.2732T>G (p.Leu911Arg) rs41295182
NM_000267.3(NF1):c.1588G>A (p.Val530Ile) rs145191978
NM_000267.3(NF1):c.4514+1G>A rs1279529138
NM_000267.3(NF1):c.4773G>A (p.Arg1591=) rs1555533268
NM_000267.3(NF1):c.6858+3A>G rs1085307885
NM_000267.3(NF1):c.7127-33TTGT[3] rs149197458
NM_000321.2(RB1):c.1072C>T (p.Arg358Ter) rs121913301
NM_000321.2(RB1):c.1666C>T (p.Arg556Ter) rs121913304
NM_000321.2(RB1):c.2356C>T (p.Pro786Ser) rs754507551
NM_000321.2(RB1):c.2566G>A (p.Asp856Asn) rs149359120
NM_000321.2(RB1):c.731T>C (p.Ile244Thr) rs147754935
NM_000368.4(TSC1):c.1231C>A (p.Leu411Ile) rs397514840
NM_000368.4(TSC1):c.1355G>C (p.Gly452Ala) rs371093730
NM_000368.4(TSC1):c.1460C>G (p.Ser487Cys) rs118203532
NM_000400.3(ERCC2):c.2150C>G (p.Ala717Gly) rs144564120
NM_000455.4(STK11):c.1045G>A (p.Glu349Lys) rs553752236
NM_000455.4(STK11):c.970C>G (p.Pro324Ala) rs549474196
NM_000455.4(STK11):c.992G>A (p.Arg331Gln) rs371264852
NM_000535.7(PMS2):c.137G>T (p.Ser46Ile) rs121434629
NM_000535.7(PMS2):c.1831dup (p.Ile611fs) rs63750250
NM_000548.5(TSC2):c.3803G>A (p.Arg1268His) rs200577441
NM_000548.5(TSC2):c.3846_3855delinsG (p.Ser1282_Gly1285delinsArg) rs587778732
NM_000548.5(TSC2):c.4046C>T (p.Ala1349Val) rs201979616
NM_000548.5(TSC2):c.4970T>A (p.Phe1657Tyr) rs878854112
NM_000548.5(TSC2):c.5336A>G (p.Gln1779Arg) rs748947919
NM_000551.3(VHL):c.241C>T (p.Pro81Ser) rs104893829
NM_000551.3(VHL):c.598C>T (p.Arg200Trp) rs28940298
NM_000553.4(WRN):c.1105C>T (p.Arg369Ter) rs17847577
NM_001083602.2(PTCH1):c.2072T>C (p.Phe691Ser) rs547954117
NM_001083602.2(PTCH1):c.4-1650G>A rs143494325
NM_001083602.2(PTCH1):c.4-1708G>A rs778460384
NM_001126112.2(TP53):c.481G>A (p.Ala161Thr) rs193920817
NM_001126112.2(TP53):c.844C>T (p.Arg282Trp) rs28934574
NM_001128849.2(SMARCA4):c.442G>A (p.Gly148Arg) rs138689221
NM_001281493.1(MSH6):c.-41_-40delinsAA rs267608079
NM_002354.2(EPCAM):c.93C>G (p.Asn31Lys) rs555329870
NM_002834.4(PTPN11):c.925A>G (p.Ile309Val) rs201787206
NM_002880.3(RAF1):c.1108+9_1108+21del rs727504451
NM_004168.4(SDHA):c.91C>T (p.Arg31Ter) rs142441643
NM_004260.3(RECQL4):c.1573del (p.Cys525fs) rs386833845
NM_004304.5(ALK):c.1283-5T>C rs377214413
NM_004304.5(ALK):c.3271G>A (p.Asp1091Asn) rs864309584
NM_004304.5(ALK):c.3837-9_3837-7dup rs373764155
NM_004360.5(CDH1):c.1225T>C (p.Trp409Arg) rs587778176
NM_004360.5(CDH1):c.2343A>T (p.Glu781Asp) rs587780119
NM_004364.4(CEBPA):c.667G>A (p.Gly223Ser) rs535980233
NM_004656.4(BAP1):c.256-3C>A rs752536342
NM_005188.3(CBL):c.1228-2A>G rs727504426
NM_005633.3(SOS1):c.2371C>A (p.Leu791Ile) rs142004123
NM_005633.3(SOS1):c.280A>G (p.Ile94Val) rs144757941
NM_005633.3(SOS1):c.3286T>A (p.Ser1096Thr) rs376722127
NM_007194.4(CHEK2):c.1100del (p.Thr367fs) rs555607708
NM_007294.3(BRCA1):c.1243G>A (p.Val415Ile) rs587782770
NM_007294.3(BRCA1):c.1534C>T (p.Leu512Phe) rs41286294
NM_007294.3(BRCA1):c.2155A>G (p.Lys719Glu) rs80357147
NM_016169.3(SUFU):c.839G>A (p.Arg280Gln) rs145704867
NM_020937.4(FANCM):c.5791C>T (p.Arg1931Ter) rs144567652
NM_020975.6(RET):c.1699G>A (p.Asp567Asn) rs147219360
NM_020975.6(RET):c.200G>A (p.Arg67His) rs192489011
NM_020975.6(RET):c.3112A>G (p.Thr1038Ala) rs201740483
NM_024426.6(WT1):c.151del (p.Ala51fs) rs776155094
NM_024675.3(PALB2):c.1478C>T (p.Pro493Leu) rs770965402
NM_024675.3(PALB2):c.3249G>C (p.Glu1083Asp)
NM_032043.2(BRIP1):c.1045G>C (p.Ala349Pro) rs149364097
NM_177438.2(DICER1):c.1124C>G (p.Pro375Arg) rs148758903
NM_177438.2(DICER1):c.2720T>C (p.Ile907Thr) rs200408568
NM_177438.2(DICER1):c.3553G>A (p.Ala1185Thr) rs150514959
NM_177438.2(DICER1):c.77C>T (p.Pro26Leu) rs201358110

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