ClinVar Miner

Variants with conflicting interpretations studied for Noonan syndrome with multiple lentigines

Coded as:
Minimum review status of the submission for Noonan syndrome with multiple lentigines: Y axis collection method of the submission for Noonan syndrome with multiple lentigines:
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
1 74 8 30 20 0 1 52

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
Noonan syndrome with multiple lentigines pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 8 6 1 0 0
uncertain significance 0 0 0 16 9
likely benign 0 0 1 0 24

Condition to condition summary #

Total conditions: 19
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
not specified 0 4 0 22 14 0 0 36
Rasopathy 0 7 4 16 10 0 1 31
not provided 0 9 4 10 6 0 0 20
Cardiovascular phenotype 0 0 0 4 4 0 0 8
Noonan syndrome 0 116 3 4 0 0 0 4
History of neurodevelopmental disorder 0 0 0 1 2 0 0 3
LEOPARD syndrome 1 0 1 3 0 0 0 0 3
Cardio-facio-cutaneous syndrome 0 25 1 1 0 0 0 2
Cardiofaciocutaneous syndrome 1 0 0 1 1 0 0 0 2
LEOPARD syndrome 2 0 0 2 0 0 0 0 2
Noonan syndrome 5 0 0 2 0 0 0 0 2
Adenocarcinoma of stomach 0 0 0 1 0 0 0 1
Cardiofaciocutaneous syndrome 1; Lung cancer; Noonan syndrome 1; LEOPARD syndrome 3; Noonan syndrome 7 0 0 1 0 0 0 0 1
Inborn genetic diseases 0 1 1 0 0 0 0 1
LEOPARD syndrome 2; Noonan syndrome 5; Cardiomyopathy, dilated, 1NN 0 0 1 0 0 0 0 1
LEOPARD syndrome 3 0 0 1 0 0 0 0 1
Lung adenocarcinoma 0 0 0 1 0 0 0 1
Malignant melanoma of skin 0 0 0 1 0 0 0 1
Neoplasm of the large intestine 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 52
Download table as spreadsheet
HGVS dbSNP
NM_002834.4(PTPN11):c.*41_*46del rs886048967
NM_002834.4(PTPN11):c.*50C>T rs730880328
NM_002834.4(PTPN11):c.-273G>A rs58805176
NM_002834.4(PTPN11):c.1093-9C>A rs12301915
NM_002834.4(PTPN11):c.1381G>A (p.Ala461Thr) rs121918468
NM_002834.4(PTPN11):c.1403C>T (p.Thr468Met) rs121918457
NM_002834.4(PTPN11):c.1449T>G (p.Gly483=) rs143238917
NM_002834.4(PTPN11):c.1517A>C (p.Gln506Pro) rs397507548
NM_002834.4(PTPN11):c.1650G>A (p.Ala550=) rs374896287
NM_002834.4(PTPN11):c.255C>T (p.His85=) rs61736914
NM_002834.4(PTPN11):c.48A>G (p.Ala16=) rs372736227
NM_002834.4(PTPN11):c.53A>G (p.Asn18Ser) rs587778635
NM_002834.4(PTPN11):c.951G>A (p.Lys317=) rs576405446
NM_002880.3(RAF1):c.-204G>C rs547543588
NM_002880.3(RAF1):c.-267G>A rs116247741
NM_002880.3(RAF1):c.-281C>G rs61761285
NM_002880.3(RAF1):c.-337_-336delAG rs527774250
NM_002880.3(RAF1):c.-416C>G rs61730434
NM_002880.3(RAF1):c.119G>A (p.Arg40His) rs192632236
NM_002880.3(RAF1):c.125C>T (p.Ala42Val) rs11549992
NM_002880.3(RAF1):c.1472C>T (p.Thr491Ile) rs80338799
NM_002880.3(RAF1):c.1669-13T>C rs147475396
NM_002880.3(RAF1):c.1755A>G (p.Val585=) rs3730296
NM_002880.3(RAF1):c.1830A>G (p.Gln610=) rs141791080
NM_002880.3(RAF1):c.1837C>G (p.Leu613Val) rs80338797
NM_002880.3(RAF1):c.1914G>A (p.Thr638=) rs144876026
NM_002880.3(RAF1):c.21T>C (p.Ala7=) rs886057915
NM_002880.3(RAF1):c.321-14T>A rs3730270
NM_002880.3(RAF1):c.321-14dupT rs202103447
NM_002880.3(RAF1):c.680+6T>C rs371846795
NM_002880.3(RAF1):c.770C>T (p.Ser257Leu) rs80338796
NM_002880.3(RAF1):c.909A>C (p.Thr303=) rs5746219
NM_002880.3(RAF1):c.923C>T (p.Pro308Leu) rs5746220
NM_004333.4(BRAF):c.*7T>C rs727502903
NM_004333.4(BRAF):c.-19C>T rs71645935
NM_004333.4(BRAF):c.2128-5delT rs373442098
NM_004333.4(BRAF):c.2128-5dupT rs373442098
NM_004333.4(BRAF):c.721A>C (p.Thr241Pro) rs387906661
NM_004333.4(BRAF):c.735A>T (p.Leu245Phe) rs397507466
NM_004333.4(BRAF):c.981-14C>A rs200002171
NM_004333.5(BRAF):c.-5A>G rs71645936
NM_004333.5(BRAF):c.1024A>G (p.Ile342Val) rs201481342
NM_004333.5(BRAF):c.1068A>G (p.Gln356=) rs143335467
NM_004333.5(BRAF):c.1227A>G (p.Ser409=) rs145035762
NM_004333.5(BRAF):c.1332G>A (p.Arg444=) rs56101602
NM_004333.5(BRAF):c.1383A>G (p.Gln461=) rs56216404
NM_004333.5(BRAF):c.1694+14G>A rs184144181
NM_004333.5(BRAF):c.2235A>G (p.Leu745=) rs56046546
NM_004333.5(BRAF):c.36G>A (p.Ala12=) rs397507454
NM_004333.5(BRAF):c.375T>G (p.Ser125=) rs201507202
NM_004333.5(BRAF):c.708C>T (p.Asn236=) rs138333692
NM_004333.5(BRAF):c.78G>T (p.Glu26Asp) rs371877084

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