ClinVar Miner

Variants with conflicting interpretations studied for TSC2-related condition

Minimum review status of the submission for TSC2-related condition: Collection method of the submission for TSC2-related condition:
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 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
109 101 2 51 51 0 0 88

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
TSC2-related condition pathogenic uncertain significance likely benign benign
likely pathogenic 1 0 0 0
uncertain significance 0 1 12 2
likely benign 0 35 1 43
benign 0 2 7 0

Condition to condition summary #

Total conditions: 3
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
not provided 0 90 2 38 45 0 0 73
not specified 0 39 0 29 9 0 0 38
Hirschsprung disease, susceptibility to, 1 0 0 0 0 1 0 0 1

All variants with conflicting interpretations #

Total variants: 88
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000548.5(TSC2):c.5359G>A (p.Gly1787Ser) rs45517419 0.00264
NM_000548.5(TSC2):c.2565C>T (p.His855=) rs143537386 0.00138
NM_000548.5(TSC2):c.1318G>A (p.Gly440Ser) rs45484298 0.00111
NM_000548.5(TSC2):c.2784C>T (p.Pro928=) rs45517267 0.00086
NM_000548.5(TSC2):c.1860G>A (p.Leu620=) rs45492397 0.00084
NM_000548.5(TSC2):c.2979G>A (p.Thr993=) rs45517277 0.00083
NM_000548.5(TSC2):c.4007C>T (p.Ser1336Leu) rs148527903 0.00067
NM_000548.5(TSC2):c.2032G>A (p.Ala678Thr) rs200494044 0.00061
NM_000548.5(TSC2):c.1609C>T (p.Arg537Cys) rs142257684 0.00054
NM_000548.5(TSC2):c.5312C>T (p.Pro1771Leu) rs137854214 0.00048
NM_000548.5(TSC2):c.2296G>A (p.Val766Met) rs150672640 0.00041
NM_000548.5(TSC2):c.4869C>T (p.Thr1623=) rs150239180 0.00041
NM_000548.5(TSC2):c.482-27C>T rs200473689 0.00037
NM_000548.5(TSC2):c.1512C>G (p.Val504=) rs146359990 0.00035
NM_000548.5(TSC2):c.681C>T (p.Cys227=) rs45443205 0.00034
NM_000548.5(TSC2):c.2743-3C>A rs45517264 0.00033
NM_000548.5(TSC2):c.4272C>T (p.Asp1424=) rs371541319 0.00032
NM_000548.5(TSC2):c.3430G>A (p.Val1144Met) rs45517294 0.00031
NM_000548.5(TSC2):c.1292C>T (p.Ala431Val) rs202187148 0.00030
NM_000548.5(TSC2):c.4680C>T (p.Ala1560=) rs139507276 0.00029
NM_000548.5(TSC2):c.4105C>T (p.Arg1369Trp) rs45517328 0.00026
NM_000548.5(TSC2):c.4929C>T (p.Asn1643=) rs45517381 0.00023
NM_000548.5(TSC2):c.4045G>A (p.Ala1349Thr) rs146239734 0.00022
NM_000548.5(TSC2):c.167A>G (p.Asn56Ser) rs144165984 0.00021
NM_000548.5(TSC2):c.3420C>T (p.Gly1140=) rs373968155 0.00021
NM_000548.5(TSC2):c.4044C>T (p.His1348=) rs137854084 0.00018
NM_000548.5(TSC2):c.4905C>T (p.Cys1635=) rs397514999 0.00017
NM_000548.5(TSC2):c.5035G>A (p.Glu1679Lys) rs370404391 0.00017
NM_000548.5(TSC2):c.1244C>T (p.Ala415Val) rs374936223 0.00016
NM_000548.5(TSC2):c.3475C>T (p.Arg1159Trp) rs45517295 0.00016
NM_000548.5(TSC2):c.1939G>A (p.Asp647Asn) rs45509392 0.00015
NM_000548.5(TSC2):c.4809C>T (p.Asp1603=) rs147578602 0.00015
NM_000548.5(TSC2):c.1947-3C>T rs201106259 0.00014
NM_000548.5(TSC2):c.3379C>T (p.Arg1127Trp) rs373939435 0.00014
NM_000548.5(TSC2):c.3491C>T (p.Ala1164Val) rs45448801 0.00014
NM_000548.5(TSC2):c.5185C>T (p.Arg1729Cys) rs45517409 0.00014
NM_000548.5(TSC2):c.223G>A (p.Glu75Lys) rs145470784 0.00013
NM_000548.5(TSC2):c.3140T>C (p.Val1047Ala) rs45517284 0.00013
NM_000548.5(TSC2):c.3919G>A (p.Glu1307Lys) rs62642481 0.00012
NM_000548.5(TSC2):c.3557A>G (p.Tyr1186Cys) rs137854421 0.00011
NM_000548.5(TSC2):c.4579T>C (p.Phe1527Leu) rs45514391 0.00011
NM_000548.5(TSC2):c.-30+2T>C rs796053514 0.00010
NM_000548.5(TSC2):c.1203C>T (p.His401=) rs199665674 0.00009
NM_000548.5(TSC2):c.4047G>A (p.Ala1349=) rs45468491 0.00009
NM_000548.5(TSC2):c.5142G>A (p.Gln1714=) rs147147042 0.00009
NM_000548.5(TSC2):c.2009C>T (p.Pro670Leu) rs397515288 0.00008
NM_000548.5(TSC2):c.3287C>T (p.Ser1096Phe) rs140772300 0.00008
NM_000548.5(TSC2):c.4136C>T (p.Ser1379Leu) rs137854065 0.00007
NM_000548.5(TSC2):c.2978C>T (p.Thr993Met) rs137854410 0.00006
NM_000548.5(TSC2):c.4683C>T (p.Ile1561=) rs145033857 0.00006
NM_000548.5(TSC2):c.4795G>A (p.Val1599Met) rs772687631 0.00006
NM_000548.5(TSC2):c.5117G>A (p.Arg1706His) rs45517392 0.00006
NM_000548.5(TSC2):c.5368G>A (p.Val1790Met) rs200140994 0.00006
NM_000548.5(TSC2):c.648+6T>C rs372007135 0.00006
NM_000548.5(TSC2):c.4225C>T (p.Arg1409Trp) rs45517333 0.00005
NM_000548.5(TSC2):c.5186G>A (p.Arg1729His) rs760395277 0.00005
NM_000548.5(TSC2):c.2539C>T (p.Leu847=) rs377300009 0.00004
NM_000548.5(TSC2):c.3710C>T (p.Ala1237Val) rs753907159 0.00004
NM_000548.5(TSC2):c.5308C>T (p.Pro1770Ser) rs761181064 0.00004
NM_000548.5(TSC2):c.861G>C (p.Glu287Asp) rs192567788 0.00004
NM_000548.5(TSC2):c.299C>T (p.Ala100Val) rs375824753 0.00003
NM_000548.5(TSC2):c.3036C>T (p.Asp1012=) rs144997264 0.00003
NM_000548.5(TSC2):c.4812C>A (p.Gly1604=) rs397515103 0.00003
NM_000548.5(TSC2):c.583A>G (p.Ile195Val) rs148325559 0.00003
NM_000548.5(TSC2):c.2404A>G (p.Ser802Gly) rs200929621 0.00002
NM_000548.5(TSC2):c.3270C>T (p.Ser1090=) rs754951889 0.00002
NM_000548.5(TSC2):c.354C>G (p.Val118=) rs762228318 0.00002
NM_000548.5(TSC2):c.3989C>T (p.Thr1330Met) rs397515209 0.00002
NM_000548.5(TSC2):c.4077C>T (p.Ile1359=) rs150999168 0.00002
NM_000548.5(TSC2):c.5161-8G>A rs374674097 0.00002
NM_000548.5(TSC2):c.5251C>T (p.Arg1751Cys) rs781630603 0.00002
NM_000548.5(TSC2):c.*4C>T rs368282661 0.00001
NM_000548.5(TSC2):c.2035G>A (p.Val679Met) rs746315218 0.00001
NM_000548.5(TSC2):c.2046G>A (p.Gly682=) rs749536123 0.00001
NM_000548.5(TSC2):c.256G>A (p.Ala86Thr) rs1190158836 0.00001
NM_000548.5(TSC2):c.2586G>A (p.Ala862=) rs752865665 0.00001
NM_000548.5(TSC2):c.5203A>G (p.Ile1735Val) rs781407050 0.00001
NM_000548.5(TSC2):c.576C>T (p.Asp192=) rs761704292 0.00001
NM_000548.5(TSC2):c.1134G>A (p.Pro378=) rs754343186
NM_000548.5(TSC2):c.1283_1285del (p.Ser428del) rs137853983
NM_000548.5(TSC2):c.3126G>T (p.Pro1042=) rs36078782
NM_000548.5(TSC2):c.3358G>C (p.Val1120Leu) rs1053311636
NM_000548.5(TSC2):c.3846_3855delinsG (p.Ser1282_Gly1285delinsArg) rs587778732
NM_000548.5(TSC2):c.4023C>A (p.Ser1341Arg) rs45462593
NM_000548.5(TSC2):c.4107G>A (p.Arg1369=) rs201688447
NM_000548.5(TSC2):c.5094C>A (p.Ser1698Arg) rs45514196
NM_000548.5(TSC2):c.5106C>T (p.Ile1702=) rs45483700
NM_000548.5(TSC2):c.5397G>A (p.Ser1799=) rs1051771

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