ClinVar Miner

Variants from Clingen PTEN Variant Curation Expert Panel, Clingen with conflicting interpretations

Location: United States  Primary collection method: curation
Minimum review status of the submission from Clingen PTEN Variant Curation Expert Panel, Clingen: Collection method of the submission from Clingen PTEN Variant Curation Expert Panel, Clingen:
Minimum review status of the other submission: Collection method of the other submission:
Minimum conflict level:

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
48 86 0 41 18 0 39 90

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, Clingen pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 15 7 0 0
likely pathogenic 15 0 20 0 0
uncertain significance 4 6 0 10 1
likely benign 0 1 8 0 10
benign 1 0 0 1 0

Submitter to submitter summary #

Total submitters: 14
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
Labcorp Genetics (formerly Invitae), Labcorp 0 92 0 31 14 0 29 74
Mendelics 0 4 0 4 4 0 0 8
All of Us Research Program, National Institutes of Health 0 22 0 0 6 0 0 6
Department of Pathology and Laboratory Medicine, Sinai Health System 0 0 0 0 0 0 6 6
Herman Laboratory, Nationwide Children's Hospital 0 3 0 2 0 0 2 4
Illumina Laboratory Services, Illumina 0 3 0 2 0 0 0 2
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 4 0 2 0 0 0 2
Genetics Laboratory, Great Ormond Street Hospital NHS Foundation Trust, North Thames Genomic Laboratory Hub 0 2 0 1 0 0 0 1
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia 0 0 0 0 1 0 0 1
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center 0 0 0 1 0 0 0 1
King Laboratory, University of Washington 0 0 0 0 0 0 1 1
Medical Molecular Genetics, University of Birmingham 0 0 0 0 0 0 1 1
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 0 3 0 1 0 0 0 1
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 90
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_001126049.2(KLLN):c.-898G>A rs538728843 0.00262
NM_000314.8(PTEN):c.132C>T (p.Gly44=) rs150651961 0.00166
NM_000314.8(PTEN):c.1104T>C (p.Asp368=) rs35979531 0.00151
NM_001126049.2(KLLN):c.-840G>A rs563841270 0.00036
NM_000314.8(PTEN):c.882T>G (p.Ser294Arg) rs143335584 0.00029
NM_000314.8(PTEN):c.-835C>T rs587779994 0.00011
NM_000314.8(PTEN):c.235G>A (p.Ala79Thr) rs202004587 0.00011
NM_000314.8(PTEN):c.579G>A (p.Leu193=) rs568851024 0.00010
NM_000314.8(PTEN):c.892C>G (p.Gln298Glu) rs371387815 0.00009
NM_000314.8(PTEN):c.720C>T (p.Tyr240=) rs190070312 0.00005
NM_000314.8(PTEN):c.-765G>A rs587776674 0.00003
NM_000314.8(PTEN):c.-799G>C rs587779992 0.00003
NM_000314.8(PTEN):c.1061C>A (p.Pro354Gln) rs375709098 0.00003
NM_000314.8(PTEN):c.1078A>G (p.Ser360Gly) rs587781273 0.00002
NM_000314.8(PTEN):c.253+4G>A rs1060500112 0.00001
NM_000314.8(PTEN):c.685T>A (p.Ser229Thr) rs587781998 0.00001
NM_000314.8(PTEN):c.78C>T (p.Thr26=) rs786201280 0.00001
NM_000314.8(PTEN):c.80-5C>T rs1060503842 0.00001
NM_000314.8(PTEN):c.-802G>A rs876661166
NM_000314.8(PTEN):c.-862G>T rs587776675
NM_000314.8(PTEN):c.-931G>A rs587781959
NM_000314.8(PTEN):c.1004G>A (p.Arg335Gln) rs1085308040
NM_000314.8(PTEN):c.100G>C (p.Ala34Pro) rs1589617199
NM_000314.8(PTEN):c.1027-1852A>G rs1194768011
NM_000314.8(PTEN):c.1027-4C>G rs587782788
NM_000314.8(PTEN):c.105G>A (p.Met35Ile) rs1554893782
NM_000314.8(PTEN):c.106G>A (p.Gly36Arg) rs786204854
NM_000314.8(PTEN):c.106G>C (p.Gly36Arg) rs786204854
NM_000314.8(PTEN):c.107G>A (p.Gly36Glu) rs1554893792
NM_000314.8(PTEN):c.1212A>C (p.Ter404Cys) rs876660879
NM_000314.8(PTEN):c.1212A>T (p.Ter404Cys) rs876660879
NM_000314.8(PTEN):c.140G>A (p.Arg47Lys) rs1057518425
NM_000314.8(PTEN):c.149T>C (p.Ile50Thr) rs1554893824
NM_000314.8(PTEN):c.152ATG[1] (p.Asp52del) rs1589617371
NM_000314.8(PTEN):c.165-1G>A rs786203847
NM_000314.8(PTEN):c.182A>G (p.His61Arg) rs398123316
NM_000314.8(PTEN):c.209+4A>G rs2132232446
NM_000314.8(PTEN):c.209T>C (p.Leu70Pro) rs121909226
NM_000314.8(PTEN):c.210-7_210-3del rs587780544
NM_000314.8(PTEN):c.334C>G (p.Leu112Val) rs2132242699
NM_000314.8(PTEN):c.338G>T (p.Ser113Ile) rs587781254
NM_000314.8(PTEN):c.355G>T (p.Val119Phe) rs139767111
NM_000314.8(PTEN):c.367C>G (p.His123Asp) rs786204931
NM_000314.8(PTEN):c.373A>G (p.Lys125Glu) rs1554898127
NM_000314.8(PTEN):c.392C>T (p.Thr131Ile) rs397514560
NM_000314.8(PTEN):c.395G>A (p.Gly132Asp) rs121909241
NM_000314.8(PTEN):c.39_41del (p.Arg15del) rs1114167625
NM_000314.8(PTEN):c.402G>C (p.Met134Ile) rs1114167676
NM_000314.8(PTEN):c.408T>G (p.Cys136Trp) rs869312776
NM_000314.8(PTEN):c.40A>G (p.Arg14Gly) rs1085308047
NM_000314.8(PTEN):c.422A>C (p.His141Pro) rs863224666
NM_000314.8(PTEN):c.42G>A (p.Arg14=) rs1064794513
NM_000314.8(PTEN):c.44G>A (p.Arg15Lys) rs398123324
NM_000314.8(PTEN):c.44G>C (p.Arg15Thr) rs398123324
NM_000314.8(PTEN):c.476G>A (p.Arg159Lys) rs1114167673
NM_000314.8(PTEN):c.492+1G>T rs1554898242
NM_000314.8(PTEN):c.492+2T>G rs1554898244
NM_000314.8(PTEN):c.493-7C>T rs1554900492
NM_000314.8(PTEN):c.511C>G (p.Gln171Glu) rs786204864
NM_000314.8(PTEN):c.512A>G (p.Gln171Arg) rs786204865
NM_000314.8(PTEN):c.521A>G (p.Tyr174Cys) rs864622341
NM_000314.8(PTEN):c.526TAT[2] (p.Tyr178del) rs587780711
NM_000314.8(PTEN):c.530A>G (p.Tyr177Cys) rs1564837839
NM_000314.8(PTEN):c.577C>T (p.Leu193=) rs772631069
NM_000314.8(PTEN):c.610C>G (p.Pro204Ala) rs786204868
NM_000314.8(PTEN):c.633C>G (p.Cys211Trp) rs121909232
NM_000314.8(PTEN):c.634+5G>C rs138336847
NM_000314.8(PTEN):c.635-3C>G rs1085308056
NM_000314.8(PTEN):c.64G>C (p.Asp22His) rs876660420
NM_000314.8(PTEN):c.67T>G (p.Leu23Val) rs876661244
NM_000314.8(PTEN):c.70G>C (p.Asp24His) rs786201995
NM_000314.8(PTEN):c.722T>C (p.Phe241Ser) rs121909240
NM_000314.8(PTEN):c.737C>T (p.Pro246Leu) rs587782350
NM_000314.8(PTEN):c.752G>T (p.Gly251Val) rs1554825226
NM_000314.8(PTEN):c.755A>G (p.Asp252Gly) rs121909239
NM_000314.8(PTEN):c.761_765del (p.Lys254fs) rs606231169
NM_000314.8(PTEN):c.79+7A>T rs374331677
NM_000314.8(PTEN):c.80-1G>C rs786204914
NM_000314.8(PTEN):c.801G>T (p.Lys267Asn) rs1554825266
NM_000314.8(PTEN):c.802-2del rs886047397
NM_000314.8(PTEN):c.802-3T>A rs587780712
NM_000314.8(PTEN):c.80A>C (p.Tyr27Ser) rs886041877
NM_000314.8(PTEN):c.80A>G (p.Tyr27Cys) rs886041877
NM_000314.8(PTEN):c.830C>G (p.Thr277Arg) rs398123329
NM_000314.8(PTEN):c.91A>G (p.Asn31Asp) rs1859093459
NM_000314.8(PTEN):c.94ATT[1] (p.Ile33del) rs1554893765
NM_000314.8(PTEN):c.959T>C (p.Leu320Ser) rs1114167667
NM_000314.8(PTEN):c.964A>T (p.Lys322Ter) rs786202004
NM_001126049.2(KLLN):c.-794_-783del rs587781340
NM_001126049.2(KLLN):c.-812G>A rs587779981

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