ClinVar Miner

Variants from St. Jude 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 St. Jude Clinical Genomics Lab, St. Jude Children's Research Hospital: Collection method of the submission from St. Jude 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 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
193 25 2 17 25 1 2 41

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
St. Jude Clinical Genomics Lab, St. Jude Children's Research Hospital pathogenic likely pathogenic uncertain significance likely benign benign risk factor
pathogenic 0 2 0 0 0 1
likely pathogenic 1 0 2 0 0 0
uncertain significance 0 0 1 10 5 0
likely benign 0 0 8 0 10 0
benign 0 0 4 4 1 0

Submitter to submitter summary #

Total submitters: 23
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
Invitae 0 17 0 8 6 0 0 14
Illumina Clinical Services Laboratory,Illumina 0 5 0 5 5 0 0 10
GeneDx 0 7 0 1 4 0 2 7
Mendelics 0 10 0 3 4 0 0 7
Integrated Genetics/Laboratory Corporation of America 0 3 0 0 4 0 0 4
CSER _CC_NCGL, University of Washington 0 0 0 0 2 0 0 2
Service de Génétique Moléculaire,Hôpital Robert Debré 0 1 0 0 2 0 0 2
CeGaT Praxis fuer Humangenetik Tuebingen 0 2 0 1 1 0 0 2
OMIM 0 3 0 0 0 1 0 1
Baylor Genetics 0 0 0 0 1 0 0 1
Athena Diagnostics Inc 0 0 0 0 1 0 0 1
Biesecker Lab/Clinical Genomics Section,National Institutes of Health 0 0 1 0 0 0 0 1
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories 0 5 0 0 1 0 0 1
PreventionGenetics, PreventionGenetics 0 2 0 0 1 0 0 1
Counsyl 0 1 0 0 1 0 0 1
Foulkes Cancer Genetics LDI, Lady Davis Institute for Medical Research 0 0 0 1 0 0 0 1
Fulgent Genetics,Fulgent Genetics 0 1 0 0 1 0 0 1
Quest Diagnostics Nichols Institute San Juan Capistrano 0 4 0 0 1 0 0 1
International Society for Gastrointestinal Hereditary Tumours (InSiGHT) 0 1 1 0 0 0 0 1
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics 0 0 0 0 1 0 0 1
Database of Curated Mutations (DoCM) 0 0 0 1 0 0 0 1
Department of Pathology and Laboratory Medicine,Sinai Health System 0 2 0 1 0 0 0 1
University of Washington Department of Laboratory Medicine, University of Washington 0 5 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 41
Download table as spreadsheet
HGVS dbSNP
NM_000038.6(APC):c.2476T>G (p.Leu826Val) rs145245264
NM_000038.6(APC):c.6679G>T (p.Gly2227Cys) rs367905430
NM_000051.3(ATM):c.1229T>C (p.Val410Ala) rs56128736
NM_000051.4(ATM):c.3925G>A (p.Ala1309Thr) rs149711770
NM_000059.3(BRCA2):c.5896C>T (p.His1966Tyr) rs80358822
NM_000059.4(BRCA2):c.1909+9_1909+10del rs527732001
NM_000059.4(BRCA2):c.7504C>T (p.Arg2502Cys) rs55716624
NM_000251.3(MSH2):c.1787A>G (p.Asn596Ser) rs41295288
NM_000264.5(PTCH1):c.2270T>C (p.Phe757Ser) rs547954117
NM_000267.3(NF1):c.6858+3A>G rs1085307885
NM_000321.2(RB1):c.1072C>T (p.Arg358Ter) rs121913301
NM_000321.2(RB1):c.731T>C (p.Ile244Thr) rs147754935
NM_000400.3(ERCC2):c.2150C>G (p.Ala717Gly) rs144564120
NM_000455.4(STK11):c.1045G>A (p.Glu349Lys) rs553752236
NM_000535.7(PMS2):c.1831dup (p.Ile611fs) rs63750250
NM_000546.5(TP53):c.319T>C (p.Tyr107His) rs368771578
NM_000546.6(TP53):c.869G>A (p.Arg290His) rs55819519
NM_000548.5(TSC2):c.5336A>G (p.Gln1779Arg) rs748947919
NM_001354630.1(MLH1):c.1732-878_1732-877delinsGC rs35502531
NM_002354.2(EPCAM):c.93C>G (p.Asn31Lys) rs555329870
NM_002485.5(NBN):c.283G>A (p.Asp95Asn) rs61753720
NM_002755.4(MAP2K1):c.1068+12_1068+15del rs397516788
NM_004360.5(CDH1):c.2343A>T (p.Glu781Asp) rs587780119
NM_004360.5(CDH1):c.2413G>A (p.Asp805Asn) rs200894246
NM_004360.5(CDH1):c.892G>A (p.Ala298Thr) rs142822590
NM_004364.4(CEBPA):c.667G>A (p.Gly223Ser) rs535980233
NM_004380.3(CREBBP):c.2678C>T (p.Ser893Leu) rs142047649
NM_005633.3(SOS1):c.1490G>A (p.Arg497Gln) rs371314838
NM_005633.3(SOS1):c.2371C>A (p.Leu791Ile) rs142004123
NM_005633.3(SOS1):c.280A>G (p.Ile94Val) rs144757941
NM_006206.6(PDGFRA):c.661C>T (p.Leu221Phe) rs139913632
NM_007194.4(CHEK2):c.1100del (p.Thr367fs) rs555607708
NM_007294.4(BRCA1):c.1534C>T (p.Leu512Phe) rs41286294
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_177438.2(DICER1):c.1124C>G (p.Pro375Arg) rs148758903
NM_177438.2(DICER1):c.2720T>C (p.Ile907Thr) rs200408568
NM_177438.2(DICER1):c.3428T>C (p.Leu1143Pro) rs139786661
NM_177438.2(DICER1):c.3553G>A (p.Ala1185Thr) rs150514959

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