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: Y axis 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 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
299 183 1 63 24 1 28 106

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 risk factor
pathogenic 0 19 5 0 0 0
likely pathogenic 30 0 9 0 0 0
uncertain significance 12 16 1 17 2 1
likely benign 2 0 12 0 14 0
benign 0 0 2 10 0 0

Condition to condition summary #

Total conditions: 32
Download table as spreadsheet
Condition 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
Hereditary cancer-predisposing syndrome 0 162 0 23 14 0 11 47
not provided 0 81 1 20 10 0 9 38
PTEN hamartoma tumor syndrome 538 26 0 10 5 0 9 24
not specified 0 43 0 14 10 0 1 24
Cowden syndrome 1 0 44 0 17 3 0 4 23
Macrocephaly/autism syndrome 0 5 0 3 1 0 3 6
Ovarian Neoplasms 0 4 0 5 0 0 1 6
Neoplasm of brain 0 0 0 4 0 0 0 4
Adenocarcinoma of prostate 0 0 0 1 0 0 2 3
Adenocarcinoma of stomach 0 0 0 1 0 0 2 3
Glioblastoma 0 1 0 1 0 0 2 3
Inborn genetic diseases 0 2 0 1 0 0 2 3
Malignant neoplasm of body of uterus 0 0 0 1 0 0 2 3
Neoplasm of the large intestine 0 2 0 1 0 0 2 3
Uterine Carcinosarcoma 0 0 0 1 0 0 2 3
Uterine cervical neoplasms 0 0 0 1 0 0 2 3
Malignant melanoma of skin 0 0 0 1 0 0 1 2
Neoplasm of the breast 0 2 0 1 0 0 1 2
Prostate cancer, somatic 0 0 0 2 0 0 0 2
Renal cell carcinoma, papillary, 1 0 0 0 1 0 0 1 2
Small cell lung cancer 0 0 0 1 0 0 1 2
Squamous cell carcinoma of the head and neck 0 0 0 1 0 0 1 2
Squamous cell lung carcinoma 0 0 0 1 0 0 1 2
Cowden syndrome 0 2 0 0 1 0 0 1
Endometrial carcinoma 0 0 0 1 0 0 0 1
Endometrial carcinoma; Macrocephaly/autism syndrome; Meningioma, familial; Squamous cell carcinoma of the head and neck; Bannayan-Riley-Ruvalcaba syndrome; Malignant tumor of prostate; Follicular thyroid carcinoma; VACTERL association with hydrocephalus; Glioma susceptibility 2; Cowden syndrome 1; Cutaneous malignant melanoma 1 0 2 0 0 1 0 0 1
Glioma susceptibility 2 0 0 0 0 0 1 0 1
Macrocephaly/autism syndrome; Meningioma, familial; Malignant tumor of prostate; VACTERL association with hydrocephalus; Glioma susceptibility 2; PTEN hamartoma tumor syndrome; Cowden syndrome 1 0 4 0 1 0 0 0 1
Meningioma 0 0 0 0 0 0 1 1
Neoplasm 0 0 0 1 0 0 0 1
Transitional cell carcinoma of the bladder 0 0 0 0 0 0 1 1
Vater association with macrocephaly and ventriculomegaly 0 0 0 0 0 0 1 1

All variants with conflicting interpretations #

Total variants: 106
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.202T>C (p.Tyr68His) rs398123317
NM_000314.4(PTEN):c.254-1G>A rs1057520208
NM_000314.4(PTEN):c.367C>T (p.His123Tyr) rs786204931
NM_000314.4(PTEN):c.379G>A (p.Gly127Arg) rs587781255
NM_000314.4(PTEN):c.406T>C (p.Cys136Arg) rs786201044
NM_000314.4(PTEN):c.44G>A (p.Arg15Lys) rs398123324
NM_000314.4(PTEN):c.493G>A (p.Gly165Arg) rs587782603
NM_000314.4(PTEN):c.737C>T (p.Pro246Leu) rs587782350
NM_000314.4(PTEN):c.802-2delA rs886047397
NM_000314.4(PTEN):c.964A>T (p.Lys322Ter) rs786202004
NM_000314.4(PTEN):c.968dupA (p.Asn323Lysfs) rs121913291
NM_000314.6(PTEN):c.*10delT rs756681683
NM_000314.6(PTEN):c.-1026C>A rs34149102
NM_000314.6(PTEN):c.-1027C>A rs587781128
NM_000314.6(PTEN):c.-1059C>G rs144620057
NM_000314.6(PTEN):c.-121A>G rs886047395
NM_000314.6(PTEN):c.-1311T>C rs70937047
NM_000314.6(PTEN):c.-734G>A rs886047384
NM_000314.6(PTEN):c.-9C>G rs11202592
NM_000314.6(PTEN):c.1003C>T (p.Arg335Ter) rs121909231
NM_000314.6(PTEN):c.1026+1G>A rs786201041
NM_000314.6(PTEN):c.1027-2A>G rs1085308041
NM_000314.6(PTEN):c.114T>G (p.Pro38=) rs748040144
NM_000314.6(PTEN):c.1212A>T (p.Ter404Cys) rs876660879
NM_000314.6(PTEN):c.132C>T (p.Gly44=) rs150651961
NM_000314.6(PTEN):c.159A>G (p.Val53=) rs189583426
NM_000314.6(PTEN):c.165-13_165-10delGTTT rs786204877
NM_000314.6(PTEN):c.182A>G (p.His61Arg) rs398123316
NM_000314.6(PTEN):c.1A>G (p.Met1Val) rs1554890324
NM_000314.6(PTEN):c.209+4_209+7delAGTA rs398123318
NM_000314.6(PTEN):c.210-7_210-3del5 rs587780544
NM_000314.6(PTEN):c.210-9T>C rs751744545
NM_000314.6(PTEN):c.253+1G>A rs587776667
NM_000314.6(PTEN):c.253+1dup rs876660082
NM_000314.6(PTEN):c.253+2T>A rs1224040268
NM_000314.6(PTEN):c.253+5G>A rs1554897889
NM_000314.6(PTEN):c.253+5G>T rs1554897889
NM_000314.6(PTEN):c.284C>T (p.Pro95Leu) rs786204856
NM_000314.6(PTEN):c.320A>T (p.Asp107Val) rs786204858
NM_000314.6(PTEN):c.321T>C (p.Asp107=) rs372876243
NM_000314.6(PTEN):c.323T>C (p.Leu108Pro) rs1064793243
NM_000314.6(PTEN):c.360A>C (p.Ala120=) rs759485888
NM_000314.6(PTEN):c.367C>G (p.His123Asp) rs786204931
NM_000314.6(PTEN):c.388C>T (p.Arg130Ter) rs121909224
NM_000314.6(PTEN):c.389G>C (p.Arg130Pro) rs121909229
NM_000314.6(PTEN):c.395G>T (p.Gly132Val) rs121909241
NM_000314.6(PTEN):c.464A>G (p.Tyr155Cys) rs1060500126
NM_000314.6(PTEN):c.470A>G (p.Glu157Gly) rs1085308051
NM_000314.6(PTEN):c.492+14dup rs1064793690
NM_000314.6(PTEN):c.517C>T (p.Arg173Cys) rs121913293
NM_000314.6(PTEN):c.518G>A (p.Arg173His) rs121913294
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.577C>T (p.Leu193=) rs772631069
NM_000314.6(PTEN):c.579G>A (p.Leu193=) rs568851024
NM_000314.6(PTEN):c.635-3C>G rs1085308056
NM_000314.6(PTEN):c.698G>A (p.Arg233Gln) rs770025422
NM_000314.6(PTEN):c.720C>T (p.Tyr240=) rs190070312
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>A (p.Thr26=) rs786201280
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.802-2A>G rs587782455
NM_000314.6(PTEN):c.802-3delT rs34003473
NM_000314.6(PTEN):c.802delG (p.Asp268Thrfs) rs587776672
NM_000314.6(PTEN):c.80A>G (p.Tyr27Cys) rs886041877
NM_000314.6(PTEN):c.830C>G (p.Thr277Arg) rs398123329
NM_000314.6(PTEN):c.838A>G (p.Ile280Val) rs1474354667
NM_000314.6(PTEN):c.855A>G (p.Glu285=) rs751888926
NM_000314.6(PTEN):c.865_866insCT (p.Lys289Thrfs) rs1554825530
NM_000314.6(PTEN):c.882T>G (p.Ser294Arg) rs143335584
NM_000314.6(PTEN):c.97_99delATT (p.Ile33del) rs1554893765
NM_000314.7(PTEN):c.-1084C>T rs538728843
NM_000314.7(PTEN):c.-1142C>T rs563841270
NM_000314.7(PTEN):c.-246C>T rs886047393
NM_000314.7(PTEN):c.-798G>C rs587779992
NM_000314.7(PTEN):c.-909T>C rs550385924
NM_000314.7(PTEN):c.1027-1G>A rs1057517809
NM_000314.7(PTEN):c.1027-4C>G rs587782788
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.403A>G (p.Ile135Val) rs587782360
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.701G>A (p.Arg234Gln) rs121909235
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.79+7A>T rs374331677
NM_000314.7(PTEN):c.884_900del17insG (p.Leu295Argfs) rs1114167680

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.