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 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
64 46 0 17 8 0 13 34

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 2 0 0
likely pathogenic 5 0 8 0 0
uncertain significance 1 1 0 4 3
likely benign 0 0 1 0 6
benign 1 0 1 1 0

Submitter to submitter summary #

Total submitters: 8
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 47 0 14 6 0 10 30
Mendelics 0 5 0 2 2 0 1 5
Illumina Clinical Services Laboratory,Illumina 0 3 0 2 1 0 1 4
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine 0 0 0 1 0 0 0 1
King Laboratory,University of Washington 0 0 0 0 0 0 1 1
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics,Children's Hospital of Philadelphia 0 0 0 0 1 0 0 1
Medical Molecular Genetics,University of Birmingham 0 0 0 0 0 0 1 1
Herman Laboratory,Nationwide Children's Hospital 0 3 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 34
Download table as spreadsheet
HGVS dbSNP
NM_000314.7(PTEN):c.-798G>C rs587779992
NM_000314.7(PTEN):c.1104T>C (p.Asp368=) rs35979531
NM_000314.7(PTEN):c.1212A>T (p.Ter404Cys) rs876660879
NM_000314.7(PTEN):c.132C>T (p.Gly44=) rs150651961
NM_000314.7(PTEN):c.1A>G (p.Met1Val) rs1554890324
NM_000314.7(PTEN):c.284C>T (p.Pro95Leu) rs786204856
NM_000314.7(PTEN):c.287C>T (p.Pro96Leu) rs1554898074
NM_000314.7(PTEN):c.314G>A (p.Cys105Tyr) rs587782343
NM_000314.7(PTEN):c.338G>T (p.Ser113Ile) rs587781254
NM_000314.7(PTEN):c.367C>G (p.His123Asp) rs786204931
NM_000314.7(PTEN):c.389G>C (p.Arg130Pro) 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.493G>A (p.Gly165Arg) rs587782603
NM_000314.7(PTEN):c.579G>A (p.Leu193=) rs568851024
NM_000314.7(PTEN):c.599T>C (p.Phe200Ser) rs786204867
NM_000314.7(PTEN):c.720C>T (p.Tyr240=) rs190070312
NM_000314.7(PTEN):c.722T>C (p.Phe241Ser) rs121909240
NM_000314.7(PTEN):c.75G>A (p.Leu25=) rs786201506
NM_000314.7(PTEN):c.79+7A>G rs374331677
NM_000314.7(PTEN):c.802-2del rs886047397
NM_000314.7(PTEN):c.80A>G (p.Tyr27Cys) rs886041877
NM_000314.7(PTEN):c.830C>G (p.Thr277Arg) rs398123329
NM_000314.7(PTEN):c.964A>T (p.Lys322Ter) rs786202004
NM_000314.8(PTEN):c.1061C>A (p.Pro354Gln) rs375709098
NM_000314.8(PTEN):c.114T>G (p.Pro38=) rs748040144
NM_000314.8(PTEN):c.210-7_210-3del rs587780544
NM_000314.8(PTEN):c.235G>A (p.Ala79Thr) rs202004587
NM_000314.8(PTEN):c.635-3C>G rs1085308056
NM_000314.8(PTEN):c.737C>T (p.Pro246Leu) rs587782350
NM_000314.8(PTEN):c.882T>G (p.Ser294Arg) rs143335584
NM_000314.8(PTEN):c.94ATT[1] (p.Ile33del) rs1554893765
NM_001126049.2(KLLN):c.-898G>A rs538728843
NM_001304718.2(PTEN):c.-420T>C rs398123321

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