ClinVar Miner

Variants from ClinGen PTEN Variant Curation Expert Panel with conflicting interpretations

Location: United States — Primary collection method: curation
Minimum review status of the submission from ClinGen PTEN Variant Curation Expert Panel: Collection method of the submission from ClinGen PTEN Variant Curation Expert Panel:
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
0 40 0 44 15 1 24 71

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
ClinGen PTEN Variant Curation Expert Panel pathogenic likely pathogenic uncertain significance likely benign benign risk factor
pathogenic 0 7 3 0 0 0
likely pathogenic 23 0 10 0 0 0
uncertain significance 6 3 0 8 3 1
likely benign 1 1 6 0 9 0
benign 0 0 1 5 0 0

Submitter to submitter summary #

Total submitters: 31
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
Ambry Genetics 0 40 0 7 9 0 4 20
GeneDx 0 35 0 11 6 0 1 18
Invitae 0 34 0 5 3 0 8 16
OMIM 0 11 0 11 0 1 4 15
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics 0 16 0 4 0 0 3 7
Quest Diagnostics Nichols Institute San Juan Capistrano 0 8 0 4 2 0 1 7
Integrated Genetics/Laboratory Corporation of America 0 5 0 5 1 0 0 6
Color 0 17 0 2 4 0 0 6
Database of Curated Mutations (DoCM) 0 0 0 4 0 0 2 6
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 0 5 0 3 1 0 1 5
PreventionGenetics,PreventionGenetics 0 5 0 3 2 0 0 5
Mendelics 0 5 0 2 2 0 0 4
Cancer Genomic Medicine Translational Research Lab,Cleveland Clinic Genomic Medicine Institute 0 4 0 1 1 0 1 3
Counsyl 0 15 0 1 2 0 0 3
German Consortium for Hereditary Breast and Ovarian Cancer Center Cologne,University Hospital Cologne 0 0 0 3 0 0 0 3
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine 0 2 0 1 1 0 0 2
Mayo Clinic Genetic Testing Laboratories,Mayo Clinic 0 2 0 0 1 0 1 2
Illumina Clinical Services Laboratory,Illumina 0 3 0 1 1 0 0 2
CeGaT Praxis fuer Humangenetik Tuebingen 0 4 0 0 2 0 0 2
University of Washington Department of Laboratory Medicine, University of Washington 0 0 0 1 1 0 0 2
Clinical Molecular Genetics Laboratory,Johns Hopkins All Children's Hospital 0 1 0 0 1 0 0 1
Biesecker Lab/Clinical Genomics Section,National Institutes of Health 0 0 0 0 1 0 0 1
Genetic Services Laboratory, University of Chicago 0 2 0 0 1 0 0 1
Division of Genomic Diagnostics,The Children's Hospital of Philadelphia 0 0 0 0 1 0 0 1
Fulgent Genetics,Fulgent Genetics 0 5 0 0 1 0 0 1
Genomic Research Center, Shahid Beheshti University of Medical Sciences 0 0 0 0 1 0 0 1
Medical Molecular Genetics,University of Birmingham 0 0 0 0 0 0 1 1
Institute of Human Genetics,FAU Erlangen-Nuremberg 0 0 0 0 0 0 1 1
GeneKor MSA 0 0 0 0 1 0 0 1
Department of Pediatrics and Neonatology,Nagoya City University Graduate School of Medical Sciences 0 0 0 1 0 0 0 1
AlTemaimi Lab, Faculty of Medicine,Kuwait University 0 0 0 0 0 0 1 1

All variants with conflicting interpretations #

Total variants: 71
Download table as spreadsheet
HGVS dbSNP
NM_000314.6(PTEN):c.-1059C>G rs144620057
NM_000314.6(PTEN):c.165-13_165-10delGTTT rs786204877
NM_000314.6(PTEN):c.802delG (p.Asp268Thrfs) rs587776672
NM_000314.7(PTEN):c.*10del rs756681683
NM_000314.7(PTEN):c.-734G>A rs886047384
NM_000314.7(PTEN):c.-764G>A rs587776674
NM_000314.7(PTEN):c.-798G>C rs587779992
NM_000314.7(PTEN):c.-861G>T rs587776675
NM_000314.7(PTEN):c.-909T>C rs550385924
NM_000314.7(PTEN):c.-975G>C rs587780001
NM_000314.7(PTEN):c.-9C>G rs11202592
NM_000314.7(PTEN):c.1026+1G>A rs786201041
NM_000314.7(PTEN):c.1027-1G>A rs1057517809
NM_000314.7(PTEN):c.103A>G (p.Met35Val) rs876659443
NM_000314.7(PTEN):c.1104T>C (p.Asp368=) rs35979531
NM_000314.7(PTEN):c.132C>T (p.Gly44=) rs150651961
NM_000314.7(PTEN):c.165-1G>A rs786203847
NM_000314.7(PTEN):c.170T>G (p.Leu57Trp) rs786202398
NM_000314.7(PTEN):c.209+4_209+7del rs398123318
NM_000314.7(PTEN):c.210-7_210-3del rs587780544
NM_000314.7(PTEN):c.235G>A (p.Ala79Thr) rs202004587
NM_000314.7(PTEN):c.278A>G (p.His93Arg) rs121909238
NM_000314.7(PTEN):c.284C>T (p.Pro95Leu) rs786204856
NM_000314.7(PTEN):c.314G>A (p.Cys105Tyr) rs587782343
NM_000314.7(PTEN):c.320A>T (p.Asp107Val) rs786204858
NM_000314.7(PTEN):c.338G>T (p.Ser113Ile) rs587781254
NM_000314.7(PTEN):c.360A>C (p.Ala120=) rs759485888
NM_000314.7(PTEN):c.368A>G (p.His123Arg) rs121909222
NM_000314.7(PTEN):c.389G>A (p.Arg130Gln) rs121909229
NM_000314.7(PTEN):c.395G>A (p.Gly132Asp) rs121909241
NM_000314.7(PTEN):c.44G>A (p.Arg15Lys) rs398123324
NM_000314.7(PTEN):c.492+2T>G rs1554898244
NM_000314.7(PTEN):c.510T>A (p.Ser170Arg) rs121909221
NM_000314.7(PTEN):c.517C>T (p.Arg173Cys) rs121913293
NM_000314.7(PTEN):c.521A>G (p.Tyr174Cys) rs864622341
NM_000314.7(PTEN):c.545T>C (p.Leu182Ser) rs794729664
NM_000314.7(PTEN):c.564T>A (p.Tyr188Ter) rs606231170
NM_000314.7(PTEN):c.634+5G>C rs138336847
NM_000314.7(PTEN):c.651C>T (p.Val217=) rs886038278
NM_000314.7(PTEN):c.696del (p.Arg233fs) rs587776669
NM_000314.7(PTEN):c.698G>A (p.Arg233Gln) rs770025422
NM_000314.7(PTEN):c.700C>T (p.Arg234Trp) rs786201730
NM_000314.7(PTEN):c.701G>A (p.Arg234Gln) rs121909235
NM_000314.7(PTEN):c.722T>C (p.Phe241Ser) rs121909240
NM_000314.7(PTEN):c.737C>T (p.Pro246Leu) rs587782350
NM_000314.7(PTEN):c.740T>C (p.Leu247Ser) rs1057519368
NM_000314.7(PTEN):c.755A>G (p.Asp252Gly) rs121909239
NM_000314.7(PTEN):c.75G>A (p.Leu25=) rs786201506
NM_000314.7(PTEN):c.761_765del (p.Lys254fs) rs606231169
NM_000314.7(PTEN):c.78C>T (p.Thr26=) rs786201280
NM_000314.7(PTEN):c.79+20C>G rs587781291
NM_000314.7(PTEN):c.79+35C>T rs190707033
NM_000314.7(PTEN):c.79+7A>G rs374331677
NM_000314.7(PTEN):c.80-1G>C rs786204914
NM_000314.7(PTEN):c.882T>G (p.Ser294Arg) rs143335584
NM_000314.7(PTEN):c.884_900delinsG (p.Leu295fs) rs1114167680
NM_000314.7(PTEN):c.964A>T (p.Lys322Ter) rs786202004
NM_001126049.1(KLLN):c.-671A>G rs70937047
NM_001126049.1(KLLN):c.-794_-783del rs587781340
NM_001126049.1(KLLN):c.-840G>A rs563841270
NM_001126049.1(KLLN):c.-898G>A rs538728843
NM_001126049.1(KLLN):c.-956G>T rs34149102
NM_001304717.5(PTEN):c.1321+1del rs1060500110
NM_001304718.2(PTEN):c.-274G>T rs1057519724
NM_001304718.2(PTEN):c.-310_-309delinsA rs1114167641
NM_001304718.2(PTEN):c.-363C>G rs121909224
NM_001304718.2(PTEN):c.-481dup rs1114167678
NM_001304718.2(PTEN):c.-541-5489T>C rs121909226
NM_001304718.2(PTEN):c.-541-5517C>G rs121909236
NM_001304718.2(PTEN):c.-612_-610ATT[1] rs1554893765
NM_001304718.2(PTEN):c.-92C>A rs397514559

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