ClinVar Miner

Variants with conflicting interpretations studied for Noonan syndrome

Coded as:
Minimum review status of the submission for Noonan syndrome: Y axis collection method of the submission for Noonan 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
118 331 6 98 45 0 14 153

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 pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 5 31 4 0 0
likely pathogenic 36 0 6 0 0
uncertain significance 3 5 0 33 26
likely benign 0 0 5 0 38
benign 0 0 2 6 1

Condition to condition summary #

Total conditions: 54
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 provided 0 106 0 65 27 0 5 95
Rasopathy 0 84 1 49 19 0 7 75
not specified 0 31 0 38 36 0 1 73
Noonan syndrome 543 43 0 13 2 0 1 16
Cardiovascular phenotype 0 4 0 5 5 0 0 10
Noonan syndrome 1 0 32 1 6 0 0 0 7
Inborn genetic diseases 0 9 0 5 0 0 1 6
Gingival fibromatosis 0 71 0 3 2 0 0 5
Noonan syndrome 8 0 7 0 3 0 0 2 5
History of neurodevelopmental disorder 0 0 0 1 3 0 0 4
Malignant melanoma of skin 0 0 0 3 0 0 1 4
Neoplasm of the large intestine 0 2 0 3 0 0 1 4
Noonan syndrome with multiple lentigines 0 116 3 4 0 0 0 4
Adenocarcinoma of stomach 0 0 0 3 0 0 0 3
Cardiofaciocutaneous syndrome 3 0 0 0 2 0 0 1 3
Cutaneous melanoma 0 1 0 1 0 0 2 3
Malignant neoplasm of body of uterus 0 0 0 2 0 0 1 3
Multiple myeloma 0 0 0 3 0 0 0 3
Noonan syndrome 5 0 2 0 3 0 0 0 3
Noonan syndrome and Noonan-related syndrome 0 3 0 3 0 0 0 3
Primary familial hypertrophic cardiomyopathy 0 1 0 3 0 0 0 3
Acute myeloid leukemia 0 0 0 2 0 0 0 2
LEOPARD syndrome 2 0 1 0 2 0 0 0 2
LEOPARD syndrome 2; Noonan syndrome 5; Cardiomyopathy, dilated, 1NN 0 0 0 2 0 0 0 2
Lung adenocarcinoma 0 0 0 2 0 0 0 2
Metachondromatosis 0 55 0 1 1 0 0 2
Neoplasm 0 0 0 1 0 0 1 2
Noonan syndrome 3 0 17 0 2 0 0 0 2
Noonan syndrome with multiple lentigines; Noonan syndrome 0 0 0 2 0 0 0 2
Squamous cell lung carcinoma 0 0 0 2 0 0 0 2
Transitional cell carcinoma of the bladder 0 0 0 1 0 0 1 2
Astrocytoma 0 0 0 1 0 0 0 1
Cardiofaciocutaneous syndrome 1 0 1 0 1 0 0 0 1
Cardiofaciocutaneous syndrome 4 0 0 0 0 1 0 0 1
Cardiomyopathy; Dilated cardiomyopathy 0 0 0 0 1 0 0 1
Cardiomyopathy; Hypertrophic cardiomyopathy; Dilated cardiomyopathy 0 0 0 1 0 0 0 1
Chronic lymphocytic leukemia 0 0 0 1 0 0 0 1
Hepatocellular carcinoma 0 0 0 1 0 0 0 1
Hypertrophic cardiomyopathy 0 2 0 1 1 0 0 1
Juvenile myelomonocytic leukemia 0 1 0 1 0 0 0 1
LEOPARD syndrome 1 0 0 1 0 0 0 0 1
Myelodysplastic syndrome 0 0 0 1 0 0 0 1
Neoplasm of the breast 0 0 0 1 0 0 0 1
Neuroblastoma 0 0 0 1 0 0 0 1
Noonan syndrome 1; Juvenile myelomonocytic leukemia; Metachondromatosis; LEOPARD syndrome 1 0 17 0 0 1 0 0 1
Noonan syndrome 4 0 6 0 1 0 0 0 1
Noonan syndrome 7 0 0 0 1 0 0 0 1
Noonan syndrome 9 0 0 0 1 0 0 0 1
Noonan syndrome-like disorder with loose anagen hair 1 0 0 0 1 0 0 0 1
Noonan syndrome; Cardio-facio-cutaneous syndrome 0 4 0 0 0 0 1 1
Pancreatic adenocarcinoma 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 carcinoma of the skin 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: 153
Download table as spreadsheet
HGVS dbSNP
NM_001269039.2(SHOC2):c.4A>G (p.Ser2Gly) rs267607048
NM_002524.5(NRAS):c.-50A>G rs61758211
NM_002524.5(NRAS):c.225C>T (p.Gly75=) rs142739534
NM_002524.5(NRAS):c.35G>T (p.Gly12Val) rs121913237
NM_002524.5(NRAS):c.553C>T (p.Pro185Ser) rs374061873
NM_002755.3(MAP2K1):c.-2A>G rs77796976
NM_002755.3(MAP2K1):c.-31dup rs730880340
NM_002755.3(MAP2K1):c.1023-8C>T rs41306345
NM_002755.3(MAP2K1):c.364A>G (p.Asn122Asp) rs876657651
NM_002755.3(MAP2K1):c.370C>T (p.Pro124Ser) rs1057519732
NM_002755.3(MAP2K1):c.608A>G rs727503996
NM_002755.3(MAP2K1):c.694-12TC[4] rs113913469
NM_002755.3(MAP2K1):c.927A>T (p.Ala309=) rs146869577
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.1403C>T (p.Thr468Met) rs121918457
NM_002834.4(PTPN11):c.1449T>G (p.Gly483=) rs143238917
NM_002834.4(PTPN11):c.1505C>T (p.Ser502Leu) rs397507544
NM_002834.4(PTPN11):c.1510A>G (p.Met504Val) rs397507547
NM_002834.4(PTPN11):c.155C>T (p.Thr52Ile) rs397507503
NM_002834.4(PTPN11):c.1620C>T (p.His540=) rs587781132
NM_002834.4(PTPN11):c.1650G>A (p.Ala550=) rs374896287
NM_002834.4(PTPN11):c.1658C>T (p.Thr553Met) rs148176616
NM_002834.4(PTPN11):c.166A>G (p.Ile56Val) rs397507504
NM_002834.4(PTPN11):c.174C>G (p.Asn58Lys) rs397507506
NM_002834.4(PTPN11):c.178G>A (p.Gly60Ser) rs397507507
NM_002834.4(PTPN11):c.182A>C (p.Asp61Ala) rs121918461
NM_002834.4(PTPN11):c.209A>G (p.Lys70Arg) rs397516801
NM_002834.4(PTPN11):c.211T>C (p.Phe71Leu) rs397507512
NM_002834.4(PTPN11):c.214G>C (p.Ala72Pro) rs121918453
NM_002834.4(PTPN11):c.215C>G (p.Ala72Gly) rs121918454
NM_002834.4(PTPN11):c.226G>A (p.Glu76Lys) rs121918464
NM_002834.4(PTPN11):c.255C>T (p.His85=) rs61736914
NM_002834.4(PTPN11):c.328G>A (p.Glu110Lys) rs397507518
NM_002834.4(PTPN11):c.392A>G (p.Lys131Arg) rs397516805
NM_002834.4(PTPN11):c.48A>G (p.Ala16=) rs372736227
NM_002834.4(PTPN11):c.526-8C>A rs184804143
NM_002834.4(PTPN11):c.53A>G (p.Asn18Ser) rs587778635
NM_002834.4(PTPN11):c.556C>T (p.Arg186Trp) rs143433437
NM_002834.4(PTPN11):c.598A>T (p.Asn200Tyr) rs727503381
NM_002834.4(PTPN11):c.774G>T (p.Glu258Asp) rs397516809
NM_002834.4(PTPN11):c.781C>T (p.Leu261Phe) rs397507525
NM_002834.4(PTPN11):c.794G>A (p.Arg265Gln) rs376607329
NM_002834.4(PTPN11):c.802G>T (p.Gly268Cys) rs397507527
NM_002834.4(PTPN11):c.846C>G (p.Ile282Met) rs397507530
NM_002834.4(PTPN11):c.853T>C (p.Phe285Leu) rs397507531
NM_002834.4(PTPN11):c.922A>G (p.Asn308Asp) rs28933386
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.-415-1C>G rs61730434
NM_002880.3(RAF1):c.1082G>C (p.Gly361Ala) rs397516813
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.1423T>C (p.Phe475Leu) rs730881003
NM_002880.3(RAF1):c.1457A>G (p.Asp486Gly) rs397516815
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.321-21dup rs202103447
NM_002880.3(RAF1):c.680+6T>C rs371846795
NM_002880.3(RAF1):c.766A>G (p.Arg256Gly) rs397516825
NM_002880.3(RAF1):c.769T>C (p.Ser257Pro) rs727505017
NM_002880.3(RAF1):c.770C>T (p.Ser257Leu) rs80338796
NM_002880.3(RAF1):c.775T>A (p.Ser259Thr) rs3730271
NM_002880.3(RAF1):c.776C>T (p.Ser259Phe) rs397516827
NM_002880.3(RAF1):c.781C>G (p.Pro261Ala) rs121434594
NM_002880.3(RAF1):c.781C>T (p.Pro261Ser) rs121434594
NM_002880.3(RAF1):c.782C>G (p.Pro261Arg) rs397516828
NM_002880.3(RAF1):c.782C>T (p.Pro261Leu) rs397516828
NM_002880.3(RAF1):c.788T>C (p.Val263Ala) rs397516830
NM_002880.3(RAF1):c.788T>G (p.Val263Gly) rs397516830
NM_002880.3(RAF1):c.909A>C (p.Thr303=) rs5746219
NM_002880.3(RAF1):c.923C>T (p.Pro308Leu) rs5746220
NM_004333.6(BRAF):c.*7T>C rs727502903
NM_004333.6(BRAF):c.-19C>T rs71645935
NM_004333.6(BRAF):c.-5A>G rs71645936
NM_004333.6(BRAF):c.1024A>G (p.Ile342Val) rs201481342
NM_004333.6(BRAF):c.1068A>G (p.Gln356=) rs143335467
NM_004333.6(BRAF):c.1227A>G (p.Ser409=) rs145035762
NM_004333.6(BRAF):c.1332G>A (p.Arg444=) rs56101602
NM_004333.6(BRAF):c.1383A>G (p.Gln461=) rs56216404
NM_004333.6(BRAF):c.1455G>T (p.Leu485Phe) rs180177036
NM_004333.6(BRAF):c.1513C>T (p.Leu505Phe) rs397507477
NM_004333.6(BRAF):c.1694+14G>A rs184144181
NM_004333.6(BRAF):c.1796C>T (p.Thr599Ile) rs121913375
NM_004333.6(BRAF):c.2128-15dup rs373442098
NM_004333.6(BRAF):c.2128-5del rs373442098
NM_004333.6(BRAF):c.2235A>G (p.Leu745=) rs56046546
NM_004333.6(BRAF):c.36G>A (p.Ala12=) rs397507454
NM_004333.6(BRAF):c.375T>G (p.Ser125=) rs201507202
NM_004333.6(BRAF):c.708C>T (p.Asn236=) rs138333692
NM_004333.6(BRAF):c.722C>A (p.Thr241Lys) rs387906660
NM_004333.6(BRAF):c.722C>T (p.Thr241Met) rs387906660
NM_004333.6(BRAF):c.739T>C (p.Phe247Leu) rs397516903
NM_004333.6(BRAF):c.741T>G (p.Phe247Leu) rs397509343
NM_004333.6(BRAF):c.785A>C (p.Gln262Pro) rs397516904
NM_004333.6(BRAF):c.78G>T (p.Glu26Asp) rs371877084
NM_004333.6(BRAF):c.793G>C (p.Gly265Arg) rs397516905
NM_004333.6(BRAF):c.981-14C>A rs200002171
NM_005188.3(CBL):c.1096-4_1096-1del rs397517077
NM_005188.3(CBL):c.1228-2A>G rs727504426
NM_005343.4(HRAS):c.37G>T (p.Gly13Cys) rs104894228
NM_005633.3(SOS1):c.*4C>T rs188849286
NM_005633.3(SOS1):c.1074+5G>C rs145155424
NM_005633.3(SOS1):c.1132A>G (p.Thr378Ala) rs397517146
NM_005633.3(SOS1):c.1230G>A (p.Gln410=) rs141390073
NM_005633.3(SOS1):c.1642A>C (p.Ser548Arg) rs397517149
NM_005633.3(SOS1):c.1867T>G (p.Phe623Val) rs727505093
NM_005633.3(SOS1):c.195A>C (p.Arg65=) rs7609455
NM_005633.3(SOS1):c.1989A>C (p.Ile663=) rs587781172
NM_005633.3(SOS1):c.2122G>A (p.Ala708Thr) rs140811086
NM_005633.3(SOS1):c.2183A>T (p.Lys728Ile) rs397517156
NM_005633.3(SOS1):c.2673+14T>C rs183998234
NM_005633.3(SOS1):c.3032A>G (p.Asn1011Ser) rs8192671
NM_005633.3(SOS1):c.322G>A (p.Glu108Lys) rs397517164
NM_005633.3(SOS1):c.3391+7A>G rs201982464
NM_005633.3(SOS1):c.553A>G (p.Ile185Val) rs143962515
NM_005633.3(SOS1):c.570C>T (p.Asp190=) rs55980502
NM_005633.3(SOS1):c.899G>A (p.Arg300Gln) rs754374236
NM_006049.4(SNAPC5):c.*169G>A rs150841154
NM_006049.4(SNAPC5):c.*961_*964AATA[1] rs397516788
NM_006049.4(SNAPC5):c.*967T>C rs368800650
NM_006912.6(RIT1):c.229G>A (p.Ala77Thr) rs869025191
NM_006912.6(RIT1):c.229G>C (p.Ala77Pro) rs869025191
NM_006912.6(RIT1):c.233G>A (p.Gly78Glu) rs1557960268
NM_006912.6(RIT1):c.244T>A (p.Phe82Ile) rs869025194
NM_006912.6(RIT1):c.244T>G (p.Phe82Val) rs869025194
NM_006939.4(SOS2):c.1127C>G (p.Thr376Ser) rs869320687
NM_030662.3(MAP2K2):c.1162C>T (p.Arg388Trp) rs144383241
NM_030662.3(MAP2K2):c.1187C>T (p.Thr396Met) rs117945277
NM_030662.3(MAP2K2):c.325C>G (p.Pro109Ala) rs1060502983
NM_030662.3(MAP2K2):c.844C>T (p.Pro282Ser) rs142307980
NM_033360.4(KRAS):c.*12A>G rs104894360
NM_033360.4(KRAS):c.*20T>G rs397517042
NM_033360.4(KRAS):c.*298T>G rs712
NM_033360.4(KRAS):c.*73T>C rs1137282
NM_033360.4(KRAS):c.-160A>G rs727503111
NM_033360.4(KRAS):c.13A>G (p.Lys5Glu) rs193929331
NM_033360.4(KRAS):c.15A>T (p.Lys5Asn) rs104894361
NM_033360.4(KRAS):c.198A>G (p.Ala66=) rs200229810
NM_033360.4(KRAS):c.264A>G (p.Lys88=) rs370920665
NM_033360.4(KRAS):c.5-9G>A rs12313763
NM_033360.4(KRAS):c.65A>G (p.Gln22Arg) rs727503110

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