ClinVar Miner

Variants with conflicting interpretations studied for RASopathy

Coded as:
Minimum review status of the submission for RASopathy: Collection method of the submission for RASopathy:
Minimum review status of the other submission: Collection method of the other submission:
Minimum conflict level:

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
7401 270 0 63 11 0 12 84

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
RASopathy pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 25 5 0 0
likely pathogenic 25 0 8 0 0
uncertain significance 5 8 0 11 1
likely benign 0 0 11 0 38
benign 0 0 1 38 0

Condition to condition summary #

Total conditions: 1
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
RASopathy 7401 270 0 63 11 0 12 84

All variants with conflicting interpretations #

Total variants: 84
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_005633.4(SOS1):c.3032A>G (p.Asn1011Ser) rs8192671 0.00164
NM_002880.4(RAF1):c.581+4A>G rs201776526 0.00082
NM_005633.4(SOS1):c.73C>T (p.Pro25Ser) rs139592595 0.00080
NM_030662.4(MAP2K2):c.844C>T (p.Pro282Ser) rs142307980 0.00068
NM_030662.4(MAP2K2):c.1093-6T>C rs369681843 0.00065
NM_002755.4(MAP2K1):c.69C>T (p.Thr23=) rs140749690 0.00054
NM_005633.4(SOS1):c.2371C>A (p.Leu791Ile) rs142004123 0.00053
NM_005188.4(CBL):c.1227+4C>T rs201747825 0.00050
NM_002834.5(PTPN11):c.1658C>T (p.Thr553Met) rs148176616 0.00048
NM_005633.4(SOS1):c.749T>C (p.Val250Ala) rs139290271 0.00046
NM_030662.4(MAP2K2):c.1140C>T (p.Ala380=) rs146618055 0.00034
NM_002880.4(RAF1):c.212A>G (p.Asn71Ser) rs184022679 0.00029
NM_030662.4(MAP2K2):c.525C>T (p.Ile175=) rs150833333 0.00029
NM_002834.5(PTPN11):c.333-3T>C rs146749153 0.00027
NM_002755.4(MAP2K1):c.848C>T (p.Ala283Val) rs144080051 0.00026
NM_030662.4(MAP2K2):c.1194C>T (p.Thr398=) rs144850779 0.00024
NM_002834.5(PTPN11):c.925A>G (p.Ile309Val) rs201787206 0.00023
NM_005633.4(SOS1):c.1705C>G (p.Leu569Val) rs200786705 0.00018
NM_005633.4(SOS1):c.3286T>A (p.Ser1096Thr) rs376722127 0.00017
NM_002880.4(RAF1):c.680+6T>C rs371846795 0.00013
NM_005633.4(SOS1):c.553A>G (p.Ile185Val) rs143962515 0.00012
NM_030662.4(MAP2K2):c.919+4C>T rs763424788 0.00009
NM_002880.4(RAF1):c.1141G>A (p.Asp381Asn) rs559632360 0.00008
NM_002834.5(PTPN11):c.1678C>T (p.Leu560Phe) rs397516797 0.00007
NM_004333.6(BRAF):c.92C>G (p.Ala31Gly) rs397516906 0.00006
NM_030662.4(MAP2K2):c.825G>A (p.Leu275=) rs587781027 0.00006
NM_002880.4(RAF1):c.66T>G (p.Phe22Leu) rs397516824 0.00005
NM_004333.6(BRAF):c.1150A>G (p.Arg384Gly) rs545495379 0.00004
NM_005633.4(SOS1):c.1490G>A (p.Arg497Gln) rs371314838 0.00004
NM_002755.4(MAP2K1):c.1098T>C (p.Ala366=) rs200293968 0.00003
NM_006767.4(LZTR1):c.842C>T (p.Pro281Leu) rs1390048261 0.00003
NM_002880.4(RAF1):c.1668+4A>G rs771344560 0.00002
NM_002880.4(RAF1):c.639T>C (p.Thr213=) rs397516823 0.00002
NM_004333.6(BRAF):c.622A>G (p.Ile208Val) rs727504571 0.00002
NM_005633.4(SOS1):c.1772A>G (p.Asn591Ser) rs757213444 0.00002
NM_030662.4(MAP2K2):c.535C>T (p.Arg179Trp) rs370799450 0.00002
NM_002834.5(PTPN11):c.1028G>A (p.Arg343Gln) rs535800148 0.00001
NM_002834.5(PTPN11):c.1529A>G (p.Gln510Arg) rs121918470 0.00001
NM_004333.6(BRAF):c.976A>G (p.Ile326Val) rs775040765 0.00001
NM_005633.4(SOS1):c.2010G>C (p.Leu670Phe) rs200712930 0.00001
NM_001085049.3(MRAS):c.203C>T (p.Thr68Ile) rs1576387876
NM_001085049.3(MRAS):c.68G>T (p.Gly23Val) rs1576359216
NM_002524.5(NRAS):c.173C>T (p.Thr58Ile) rs2101742052
NM_002755.4(MAP2K1):c.124C>T (p.Leu42Phe) rs397516789
NM_002755.4(MAP2K1):c.169A>C (p.Lys57Gln) rs397516790
NM_002755.4(MAP2K1):c.323G>T (p.Arg108Leu) rs727504819
NM_002755.4(MAP2K1):c.364A>G (p.Asn122Asp) rs876657651
NM_002755.4(MAP2K1):c.608A>G (p.Glu203Gly) rs727503996
NM_002834.5(PTPN11):c.1052G>A (p.Arg351Gln) rs397507534
NM_002834.5(PTPN11):c.1471C>A (p.Pro491Thr) rs397507539
NM_002834.5(PTPN11):c.155C>T (p.Thr52Ile) rs397507503
NM_002834.5(PTPN11):c.178G>C (p.Gly60Arg) rs397507507
NM_002834.5(PTPN11):c.215C>T (p.Ala72Val) rs121918454
NM_002834.5(PTPN11):c.226G>A (p.Glu76Lys) rs121918464
NM_002834.5(PTPN11):c.227A>G (p.Glu76Gly) rs121918465
NM_002834.5(PTPN11):c.53A>G (p.Asn18Ser) rs587778635
NM_002834.5(PTPN11):c.782T>A (p.Leu261His) rs765642157
NM_002834.5(PTPN11):c.782T>G (p.Leu261Arg) rs765642157
NM_002834.5(PTPN11):c.854T>A (p.Phe285Tyr) rs121918463
NM_002880.4(RAF1):c.1108+9_1108+21del rs727504451
NM_002880.4(RAF1):c.1193G>T (p.Arg398Leu) rs730880382
NM_002880.4(RAF1):c.124_125delinsAT (p.Ala42Ile) rs876657965
NM_002880.4(RAF1):c.1629G>C (p.Thr543=) rs5746244
NM_002880.4(RAF1):c.768G>T (p.Arg256Ser) rs397516826
NM_002880.4(RAF1):c.775T>C (p.Ser259Pro) rs3730271
NM_002880.4(RAF1):c.779C>A (p.Thr260Lys) rs869025501
NM_002880.4(RAF1):c.779C>T (p.Thr260Ile) rs869025501
NM_002880.4(RAF1):c.782C>G (p.Pro261Arg) rs397516828
NM_002880.4(RAF1):c.788T>C (p.Val263Ala) rs397516830
NM_002880.4(RAF1):c.788T>G (p.Val263Gly) rs397516830
NM_004333.6(BRAF):c.1781A>T (p.Asp594Val) rs121913338
NM_004333.6(BRAF):c.1802A>T (p.Lys601Ile) rs397507484
NM_004333.6(BRAF):c.722C>A (p.Thr241Lys) rs387906660
NM_004985.5(KRAS):c.108A>G (p.Ile36Met) rs727503109
NM_004985.5(KRAS):c.13A>G (p.Lys5Glu) rs193929331
NM_004985.5(KRAS):c.528GAA[1] (p.Lys180del) rs397517043
NM_005188.4(CBL):c.107ACC[6] (p.His42del) rs373212940
NM_006767.4(LZTR1):c.1234C>T (p.Arg412Cys) rs747430075
NM_006767.4(LZTR1):c.742G>A (p.Gly248Arg) rs869320686
NM_007373.4(SHOC2):c.1540+8C>T rs771283010
NM_030662.4(MAP2K2):c.291C>A (p.Ile97=) rs200918323
NM_030662.4(MAP2K2):c.401A>G (p.Tyr134Cys) rs727504370
NM_030662.4(MAP2K2):c.546G>A (p.Ala182=) rs141402203
NM_033360.4(KRAS):c.194G>T (p.Ser65Ile) rs1555194026

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