ClinVar Miner

Variants with conflicting interpretations studied for Cowden syndrome 1

Coded as:
Minimum review status of the submission for Cowden syndrome 1: Y axis collection method of the submission for Cowden syndrome 1:
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
29 52 1 28 13 0 6 43

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
Cowden syndrome 1 pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 18 5 2 0
likely pathogenic 5 0 0 0 0
uncertain significance 3 1 1 8 6
likely benign 0 0 4 0 5
benign 0 0 0 1 0

Condition to condition summary #

Total conditions: 25
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
PTEN hamartoma tumor syndrome 0 50 0 17 3 0 5 24
Hereditary cancer-predisposing syndrome 0 41 0 7 9 0 2 17
not specified 0 14 0 5 7 0 2 13
not provided 0 33 1 5 6 0 2 12
Cowden syndrome 1 116 5 0 1 0 0 2 3
Inborn genetic diseases 0 3 0 1 0 0 1 2
Neoplasm of brain 0 0 0 2 0 0 0 2
Ovarian Neoplasms 0 4 0 2 0 0 0 2
Adenocarcinoma of prostate 0 0 0 1 0 0 0 1
Adenocarcinoma of stomach 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 0 0 1 1
Glioblastoma 0 1 0 1 0 0 0 1
Macrocephaly/autism syndrome 0 4 0 0 0 0 1 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 3 0 0 0 0 1 1
Malignant melanoma of skin 0 0 0 1 0 0 0 1
Malignant neoplasm of body of uterus 0 0 0 1 0 0 0 1
Neoplasm 0 0 0 1 0 0 0 1
Neoplasm of the breast 0 1 0 1 0 0 0 1
Neoplasm of the large intestine 0 1 0 1 0 0 0 1
Renal cell carcinoma, papillary, 1 0 0 0 1 0 0 0 1
Small cell lung cancer 0 0 0 1 0 0 0 1
Squamous cell carcinoma of the head and neck 0 0 0 1 0 0 0 1
Squamous cell lung carcinoma 0 0 0 1 0 0 0 1
Uterine Carcinosarcoma 0 0 0 1 0 0 0 1
Uterine cervical neoplasms 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 43
Download table as spreadsheet
HGVS dbSNP
NM_000314.6(PTEN):c.165-13_165-10delGTTT rs786204877
NM_000314.6(PTEN):c.802delG (p.Asp268Thrfs) rs587776672
NM_000314.7(PTEN):c.*10del rs756681683
NM_000314.7(PTEN):c.*10dup rs756681683
NM_000314.7(PTEN):c.-734G>A rs886047384
NM_000314.7(PTEN):c.-764G>A rs587776674
NM_000314.7(PTEN):c.-861G>T rs587776675
NM_000314.7(PTEN):c.-9C>G rs11202592
NM_000314.7(PTEN):c.1003C>T (p.Arg335Ter) rs121909231
NM_000314.7(PTEN):c.1026+1G>A rs786201041
NM_000314.7(PTEN):c.1026+1G>C rs786201041
NM_000314.7(PTEN):c.202T>C (p.Tyr68His) rs398123317
NM_000314.7(PTEN):c.209+4_209+7del rs398123318
NM_000314.7(PTEN):c.209T>C (p.Leu70Pro) rs121909226
NM_000314.7(PTEN):c.210-39A>G rs370918174
NM_000314.7(PTEN):c.210-7_210-3del rs587780544
NM_000314.7(PTEN):c.210-9T>C rs751744545
NM_000314.7(PTEN):c.235G>A (p.Ala79Thr) rs202004587
NM_000314.7(PTEN):c.253+1G>A rs587776667
NM_000314.7(PTEN):c.253+5G>A rs1554897889
NM_000314.7(PTEN):c.254-30dup rs77494260
NM_000314.7(PTEN):c.368A>G (p.His123Arg) rs121909222
NM_000314.7(PTEN):c.388C>T (p.Arg130Ter) rs121909224
NM_000314.7(PTEN):c.389G>A (p.Arg130Gln) rs121909229
NM_000314.7(PTEN):c.395G>T (p.Gly132Val) rs121909241
NM_000314.7(PTEN):c.464A>G (p.Tyr155Cys) rs1060500126
NM_000314.7(PTEN):c.492+2T>G rs1554898244
NM_000314.7(PTEN):c.510T>A (p.Ser170Arg) rs121909221
NM_000314.7(PTEN):c.579G>A (p.Leu193=) rs568851024
NM_000314.7(PTEN):c.634+5G>C rs138336847
NM_000314.7(PTEN):c.696del (p.Arg233fs) rs587776669
NM_000314.7(PTEN):c.720C>T (p.Tyr240=) rs190070312
NM_000314.7(PTEN):c.737C>T (p.Pro246Leu) rs587782350
NM_000314.7(PTEN):c.78C>T (p.Thr26=) rs786201280
NM_000314.7(PTEN):c.79+7A>G rs374331677
NM_000314.7(PTEN):c.802-12T>C rs587781129
NM_000314.7(PTEN):c.802-2A>G rs587782455
NM_000314.7(PTEN):c.802-51_802-14del rs557364463
NM_000314.7(PTEN):c.865_866insCT (p.Lys289fs) rs1554825530
NM_000314.7(PTEN):c.882T>G (p.Ser294Arg) rs143335584
NM_000314.7(PTEN):c.968dup (p.Asn323fs) rs121913291
NM_000314.7(PTEN):c.975_988delinsCGCTT (p.Asp326_Lys330delinsAlaTer) rs1114167640
NM_001126049.1(KLLN):c.-898G>A rs538728843

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