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 26 0 33 10 0 11 48

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
pathogenic 0 5 1 0 0
likely pathogenic 16 0 6 0 0
uncertain significance 2 1 0 6 2
likely benign 1 0 4 0 8
benign 0 0 0 4 0

Submitter to submitter summary #

Total submitters: 25
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
GeneDx 0 22 0 10 5 0 1 16
Ambry Genetics 0 25 0 6 6 0 2 14
Invitae 0 14 0 5 4 0 5 14
OMIM 0 8 0 9 0 0 2 11
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics 0 10 0 3 0 0 2 5
Quest Diagnostics Nichols Institute San Juan Capistrano 0 5 0 3 2 0 0 5
PreventionGenetics 0 5 0 3 1 0 0 4
Integrated Genetics/Laboratory Corporation of America 0 3 0 3 1 0 0 4
Color 0 10 0 1 3 0 0 4
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories 0 2 0 2 1 0 0 3
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine 0 1 0 1 1 0 0 2
Counsyl 0 9 0 1 1 0 0 2
Mayo Clinic Genetic Testing Laboratories,Mayo Clinic 0 2 0 0 1 0 1 2
Database of Curated Mutations (DoCM) 0 0 0 2 0 0 0 2
German Consortium for Hereditary Breast and Ovarian Cancer Center Cologne,University Hospital Cologne 0 0 0 2 0 0 0 2
Biesecker Lab/Human Development Section,National Institutes of Health 0 0 0 0 1 0 0 1
Cancer Genomic Medicine Translational Research Lab,Cleveland Clinic Genomic Medicine Institute 0 4 0 0 0 0 1 1
Division of Genomic Diagnostics,The Children's Hospital of Philadelphia 0 0 0 0 1 0 0 1
Mendelics 0 1 0 0 1 0 0 1
Fulgent Genetics 0 2 0 0 1 0 0 1
Genomic Research Center,Shahid Beheshti University of Medical Sciences 0 0 0 0 1 0 0 1
Illumina Clinical Services Laboratory,Illumina 0 2 0 1 0 0 0 1
GeneKor MSA 0 0 0 0 1 0 0 1
AlTemaimi Lab, Faculty of Medicine,Kuwait University 0 0 0 0 0 0 1 1
University of Washington Department of Laboratory Medicine,University of Washington 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 48
Download table as spreadsheet
HGVS dbSNP
NM_000314.4(PTEN):c.-764G>A rs587776674
NM_000314.4(PTEN):c.1104T>C (p.Asp368=) rs35979531
NM_000314.4(PTEN):c.165-1G>A rs786203847
NM_000314.4(PTEN):c.44G>A (p.Arg15Lys) rs398123324
NM_000314.4(PTEN):c.737C>T (p.Pro246Leu) rs587782350
NM_000314.4(PTEN):c.964A>T (p.Lys322Ter) rs786202004
NM_000314.6(PTEN):c.*10delT rs756681683
NM_000314.6(PTEN):c.-1026C>A rs34149102
NM_000314.6(PTEN):c.-1059C>G rs144620057
NM_000314.6(PTEN):c.-1311T>C rs70937047
NM_000314.6(PTEN):c.-9C>G rs11202592
NM_000314.6(PTEN):c.1026+1G>A rs786201041
NM_000314.6(PTEN):c.132C>T (p.Gly44=) rs150651961
NM_000314.6(PTEN):c.165-13_165-10delGTTT rs786204877
NM_000314.6(PTEN):c.209+4_209+7delAGTA rs398123318
NM_000314.6(PTEN):c.360A>C (p.Ala120=) rs759485888
NM_000314.6(PTEN):c.517C>T (p.Arg173Cys) rs121913293
NM_000314.6(PTEN):c.521A>G (p.Tyr174Cys) rs864622341
NM_000314.6(PTEN):c.564T>A (p.Tyr188Ter) rs606231170
NM_000314.6(PTEN):c.75G>A (p.Leu25=) rs786201506
NM_000314.6(PTEN):c.761_765delAAGTA (p.Lys254Argfs) rs606231169
NM_000314.6(PTEN):c.78C>T (p.Thr26=) rs786201280
NM_000314.6(PTEN):c.79+35C>T rs190707033
NM_000314.6(PTEN):c.80-1G>C rs786204914
NM_000314.6(PTEN):c.801+1delG rs1060500110
NM_000314.6(PTEN):c.802delG (p.Asp268Thrfs) rs587776672
NM_000314.7(PTEN):c.-1084C>T rs538728843
NM_000314.7(PTEN):c.-1142C>T rs563841270
NM_000314.7(PTEN):c.-798G>C rs587779992
NM_000314.7(PTEN):c.-909T>C rs550385924
NM_000314.7(PTEN):c.103A>G (p.Met35Val) rs876659443
NM_000314.7(PTEN):c.170T>G (p.Leu57Trp) rs786202398
NM_000314.7(PTEN):c.181C>G (p.His61Asp) rs121909236
NM_000314.7(PTEN):c.209T>C (p.Leu70Pro) rs121909226
NM_000314.7(PTEN):c.235G>A (p.Ala79Thr) rs202004587
NM_000314.7(PTEN):c.270dup (p.Glu91Terfs) rs1114167678
NM_000314.7(PTEN):c.278A>G (p.His93Arg) rs121909238
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.500C>A (p.Thr167Asn) rs397514559
NM_000314.7(PTEN):c.510T>A (p.Ser170Arg) rs121909221
NM_000314.7(PTEN):c.651C>T (p.Val217=) rs886038278
NM_000314.7(PTEN):c.722T>C (p.Phe241Ser) rs121909240
NM_000314.7(PTEN):c.755A>G (p.Asp252Gly) rs121909239
NM_000314.7(PTEN):c.79+20C>G rs587781291
NM_000314.7(PTEN):c.79+7A>G rs374331677
NM_000314.7(PTEN):c.884_900del17insG (p.Leu295Argfs) rs1114167680

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