ClinVar Miner

Variants with conflicting interpretations studied for PTEN hamartoma tumor syndrome

Coded as:
Minimum review status of the submission for PTEN hamartoma tumor syndrome: Collection method of the submission for PTEN hamartoma tumor syndrome:
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
1577 188 0 42 24 0 30 86

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 conditions
PTEN hamartoma tumor syndrome pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 28 15 1 1
likely pathogenic 26 0 17 0 0
uncertain significance 14 18 0 24 5
likely benign 1 0 24 0 14
benign 1 0 5 14 0

Condition to condition summary #

Total conditions: 6
Download table as spreadsheet
Condition 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
PTEN hamartoma tumor syndrome 1593 175 0 40 24 0 28 83
Macrocephaly-autism syndrome; Familial meningioma; Malignant tumor of prostate; Glioma susceptibility 2; Cowden syndrome 1 0 16 0 3 3 0 1 6
Endometrial carcinoma; Macrocephaly-autism syndrome; Familial meningioma; Squamous cell carcinoma of the head and neck; Bannayan-Riley-Ruvalcaba syndrome; Malignant tumor of prostate; Thyroid cancer, nonmedullary, 2; VACTERL with hydrocephalus; Glioma susceptibility 2; Cowden syndrome 1; Melanoma, cutaneous malignant, susceptibility to, 1 0 0 0 0 1 0 0 1
Heart, malformation of; Intellectual disability 0 0 0 0 0 0 1 1
Hiatus hernia; Expressive language delay; Microcephaly; Delayed gross motor development; Mild short stature; Delayed fine motor development 0 0 0 1 0 0 0 1
Short stature; Failure to thrive; Anemia; Strabismus; Splenomegaly; Sparse hair; Neurodevelopmental delay; Thrombocytopenia 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 86
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 0.00168
NM_000314.8(PTEN):c.1104T>C (p.Asp368=) rs35979531 0.00158
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.234C>T (p.Thr78=) rs35917308 0.00016
NM_000314.8(PTEN):c.802-12T>C rs587781129 0.00015
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 0.00006
NM_000314.8(PTEN):c.*5T>C rs1006891299 0.00005
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.159A>G (p.Val53=) rs189583426 0.00003
NM_000314.8(PTEN):c.1078A>G (p.Ser360Gly) rs587781273 0.00002
NM_000314.8(PTEN):c.114T>G (p.Pro38=) rs748040144 0.00001
NM_000314.8(PTEN):c.253+4G>A rs1060500112 0.00001
NM_000314.8(PTEN):c.518G>A (p.Arg173His) rs121913294 0.00001
NM_000314.8(PTEN):c.78C>T (p.Thr26=) rs786201280 0.00001
NM_000314.8(PTEN):c.858C>G (p.Thr286=) rs876660443 0.00001
NM_000314.8(PTEN):c.-735G>A rs886047384
NM_000314.8(PTEN):c.-802G>A rs876661166
NM_000314.8(PTEN):c.1004G>A (p.Arg335Gln) rs1085308040
NM_000314.8(PTEN):c.1027-4C>G rs587782788
NM_000314.8(PTEN):c.1034T>C (p.Leu345Pro) rs1554826024
NM_000314.8(PTEN):c.1034T>G (p.Leu345Arg) rs1554826024
NM_000314.8(PTEN):c.103A>G (p.Met35Val) rs876659443
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.1092T>G (p.Ser364=) rs1355576298
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.152ATG[1] (p.Asp52del) rs1589617371
NM_000314.8(PTEN):c.16A>G (p.Lys6Glu) rs1589596143
NM_000314.8(PTEN):c.182A>G (p.His61Arg) rs398123316
NM_000314.8(PTEN):c.202T>C (p.Tyr68His) rs398123317
NM_000314.8(PTEN):c.209+2T>C rs878853937
NM_000314.8(PTEN):c.210-7_210-3del rs587780544
NM_000314.8(PTEN):c.254-3_254-2del rs1064794169
NM_000314.8(PTEN):c.284C>T (p.Pro95Leu) rs786204856
NM_000314.8(PTEN):c.314G>A (p.Cys105Tyr) rs587782343
NM_000314.8(PTEN):c.338G>T (p.Ser113Ile) rs587781254
NM_000314.8(PTEN):c.344A>G (p.Asp115Gly) rs869312775
NM_000314.8(PTEN):c.367C>G (p.His123Asp) rs786204931
NM_000314.8(PTEN):c.385G>A (p.Gly129Arg) rs786204929
NM_000314.8(PTEN):c.395G>A (p.Gly132Asp) rs121909241
NM_000314.8(PTEN):c.397G>A (p.Val133Ile) rs1859977307
NM_000314.8(PTEN):c.39_41del (p.Arg15del) rs1114167625
NM_000314.8(PTEN):c.401T>C (p.Met134Thr) rs1085308046
NM_000314.8(PTEN):c.402G>C (p.Met134Ile) rs1114167676
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.492+2T>G rs1554898244
NM_000314.8(PTEN):c.493-7C>T rs1554900492
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.522T>G (p.Tyr174Ter) rs786201867
NM_000314.8(PTEN):c.577C>T (p.Leu193=) rs772631069
NM_000314.8(PTEN):c.599T>C (p.Phe200Ser) rs786204867
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.71A>G (p.Asp24Gly) rs797044910
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.755A>G (p.Asp252Gly) rs121909239
NM_000314.8(PTEN):c.79+7A>T rs374331677
NM_000314.8(PTEN):c.80-1_80del rs1554893747
NM_000314.8(PTEN):c.80-5C>T rs1060503842
NM_000314.8(PTEN):c.802-2del rs886047397
NM_000314.8(PTEN):c.80A>C (p.Tyr27Ser) 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.964A>T (p.Lys322Ter) rs786202004
NM_000314.8(PTEN):c.96T>C (p.Ile32=)
NM_001126049.2(KLLN):c.-794_-783del rs587781340
Single allele

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