ClinVar Miner

Variants with conflicting interpretations studied for Hereditary cancer

Coded as:
Minimum review status of the submission for Hereditary cancer: Collection method of the submission for Hereditary cancer:
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
33 20 0 30 154 2 0 163

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
Hereditary cancer pathogenic likely pathogenic uncertain significance likely benign benign risk factor
pathogenic 0 1 0 0 0 0
likely pathogenic 1 0 0 0 0 0
uncertain significance 0 0 0 4 2 0
likely benign 0 0 150 0 28 2

Condition to condition summary #

Total conditions: 36
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 14 0 16 133 0 0 142
not specified 0 25 0 16 80 0 0 89
Breast and/or ovarian cancer 0 9 0 0 14 0 0 14
Hereditary nonpolyposis colorectal neoplasms 0 6 0 6 5 0 0 11
EGFR-related lung cancer 0 11 0 0 8 0 0 8
ATM-related disorder 0 2 0 0 5 0 0 5
POLE-related disorder 0 3 0 0 5 0 0 5
CHEK2-related disorder 0 0 0 0 3 0 0 3
Hirschsprung disease, susceptibility to, 1 0 1 0 0 3 0 0 3
APC-Associated Polyposis Disorders 0 3 0 0 2 0 0 2
APC-related disorder 0 0 0 0 2 0 0 2
Diffuse midline glioma, H3 K27-altered 0 0 0 0 2 0 0 2
EGFR-related disorder 0 0 0 0 2 0 0 2
MUTYH-related disorder 0 1 0 0 2 0 0 2
BARD1-related disorder 0 0 0 0 1 0 0 1
BRIP1-related disorder 0 0 0 0 1 0 0 1
Breast-ovarian cancer, familial, susceptibility to, 3; Fanconi anemia complementation group O 0 0 0 1 0 0 0 1
CDH1-related disorder 0 0 0 0 1 0 0 1
Hirschsprung disease, susceptibility to, 1; Multiple endocrine neoplasia type 2B; Pheochromocytoma; Familial medullary thyroid carcinoma; Multiple endocrine neoplasia type 2A 0 0 0 0 1 0 0 1
Leukemia, acute lymphoblastic, susceptibility to 0 0 0 0 0 1 0 1
Lynch-like syndrome 0 0 0 0 1 0 0 1
MLH1-related disorder 0 0 0 0 1 0 0 1
NF1-related disorder 0 1 0 0 1 0 0 1
PALB2-related disorder 0 2 0 0 1 0 0 1
PDGFRA-related disorder 0 0 0 1 0 0 0 1
PMS2-related disorder 0 0 0 0 1 0 0 1
POLD1-related disorder 0 1 0 0 1 0 0 1
PTEN-related disorder 0 1 0 1 0 0 0 1
Predisposition to cancer 0 0 0 0 1 0 0 1
RAD51-related disorder 0 1 0 0 1 0 0 1
RAD51D-related disorder 0 0 0 0 1 0 0 1
RECLASSIFIED - CDH1 POLYMORPHISM 0 0 0 0 0 1 0 1
RECQL-related disorder 0 1 0 0 1 0 0 1
RET-related disorder 0 0 0 0 1 0 0 1
STK11-related disorder 0 0 0 0 1 0 0 1
Triple-Negative Breast Cancer Finding 0 0 0 0 1 0 0 1

All variants with conflicting interpretations #

Total variants: 163
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_021133.4(RNASEL):c.1385G>A (p.Arg462Gln) rs486907 0.28062
NM_006206.6(PDGFRA):c.2323+1120C>T rs2291591 0.08547
NM_000465.4(BARD1):c.1972C>T (p.Arg658Cys) rs3738888 0.00736
NM_001190274.2(FBXO11):c.*1173A>T rs2020906 0.00645
NM_000222.3(KIT):c.2597-51T>C rs368272654 0.00263
NM_014967.5(FAN1):c.149T>G (p.Met50Arg) rs148404807 0.00191
NM_002875.5(RAD51):c.449G>A (p.Arg150Gln) rs121917739 0.00171
NM_002878.4(RAD51D):c.568G>A (p.Ala190Thr) rs80116829 0.00167
NM_000465.4(BARD1):c.2282G>A (p.Ser761Asn) rs142155101 0.00153
NM_002485.5(NBN):c.511A>G (p.Ile171Val) rs61754966 0.00145
NM_000057.4(BLM):c.2263A>G (p.Lys755Glu) rs142551229 0.00140
NM_000051.4(ATM):c.6176C>T (p.Thr2059Ile) rs144761622 0.00126
NM_006231.4(POLE):c.861T>A (p.Asp287Glu) rs139075637 0.00122
NM_002529.4(NTRK1):c.865C>A (p.Gln289Lys) rs137979116 0.00118
NM_000249.4(MLH1):c.-28A>G rs56198082 0.00110
NM_000057.4(BLM):c.11T>C (p.Val4Ala) rs144706057 0.00102
NM_000136.3(FANCC):c.178G>A (p.Val60Ile) rs138629441 0.00091
NM_000535.7(PMS2):c.497T>C (p.Leu166Pro) rs116349687 0.00088
NM_032444.4(SLX4):c.1372A>G (p.Lys458Glu) rs149126845 0.00087
NM_001048174.2(MUTYH):c.1192C>T (p.Arg398Cys) rs150792276 0.00081
NM_001048174.2(MUTYH):c.1424G>A (p.Gly475Glu) rs3219494 0.00076
NM_000051.4(ATM):c.6988C>G (p.Leu2330Val) rs148432863 0.00075
NM_002485.5(NBN):c.1354A>C (p.Thr452Pro) rs141137543 0.00075
NM_000535.7(PMS2):c.2149G>A (p.Val717Met) rs201671325 0.00072
NM_007194.4(CHEK2):c.320-5T>A rs121908700 0.00070
NM_000245.4(MET):c.1039G>A (p.Ala347Thr) rs200074800 0.00068
NM_000179.3(MSH6):c.663A>C (p.Glu221Asp) rs41557217 0.00064
NM_006231.4(POLE):c.4057A>G (p.Ser1353Gly) rs141619382 0.00063
NM_002691.4(POLD1):c.455C>T (p.Ala152Val) rs41563714 0.00062
NM_005228.5(EGFR):c.3467A>C (p.His1156Pro) rs149174093 0.00062
NM_000245.4(MET):c.467C>T (p.Ser156Leu) rs56311081 0.00061
NM_002485.5(NBN):c.788T>C (p.Phe263Ser) rs147626427 0.00059
NM_001042492.3(NF1):c.2033C>T (p.Pro678Leu) rs17881753 0.00058
NM_007294.4(BRCA1):c.5348T>C (p.Met1783Thr) rs55808233 0.00058
NM_000038.6(APC):c.3173A>G (p.Asp1058Gly) rs148725540 0.00056
NM_000051.4(ATM):c.6543G>T (p.Glu2181Asp) rs138828590 0.00056
NM_000057.4(BLM):c.968A>G (p.Lys323Arg) rs146504061 0.00056
NM_002907.4(RECQL):c.406G>A (p.Val136Ile) rs138278747 0.00055
NM_001048174.2(MUTYH):c.841C>T (p.Arg281Cys) rs138089183 0.00051
NM_020975.6(RET):c.405C>T (p.Gly135=) rs142345108 0.00051
NM_000179.3(MSH6):c.2667G>T (p.Gln889His) rs149945495 0.00048
NM_022725.4(FANCF):c.241G>T (p.Ala81Ser) rs145057187 0.00048
NM_006231.4(POLE):c.5659G>A (p.Val1887Met) rs114119067 0.00047
NM_017763.6(RNF43):c.575C>T (p.Pro192Leu) rs139557480 0.00046
NM_001382430.1(AKT1):c.138C>A (p.Asp46Glu) rs146875699 0.00045
NM_002691.4(POLD1):c.2052G>C (p.Gln684His) rs144143245 0.00045
NM_002878.4(RAD51D):c.932T>A (p.Ile311Asn) rs145309168 0.00041
NM_032043.3(BRIP1):c.2220G>T (p.Gln740His) rs45589637 0.00041
NM_007294.4(BRCA1):c.301+146A>C rs571713225 0.00039
NM_000136.3(FANCC):c.1374A>C (p.Arg458Ser) rs56394801 0.00038
NM_002878.4(RAD51D):c.26G>C (p.Cys9Ser) rs140825795 0.00037
NM_002907.4(RECQL):c.401C>T (p.Thr134Ile) rs150306543 0.00037
NM_000038.6(APC):c.6857C>T (p.Ala2286Val) rs200587641 0.00036
NM_005228.5(EGFR):c.3629C>T (p.Ala1210Val) rs35918369 0.00034
NM_007194.4(CHEK2):c.1312G>T (p.Asp438Tyr) rs200050883 0.00034
NM_002485.5(NBN):c.425A>G (p.Asn142Ser) rs769414 0.00033
NM_002529.4(NTRK1):c.482G>A (p.Arg161His) rs150271893 0.00031
NM_001042492.3(NF1):c.5906A>T (p.Gln1969Leu) rs143502927 0.00029
NM_000038.6(APC):c.2593C>T (p.Pro865Ser) rs192620988 0.00028
NM_000535.7(PMS2):c.1004A>G (p.Asn335Ser) rs200513014 0.00026
NM_000051.4(ATM):c.5975A>C (p.Lys1992Thr) rs150757822 0.00025
NM_005228.5(EGFR):c.2024G>A (p.Arg675Gln) rs150423237 0.00025
NM_006231.4(POLE):c.2683G>A (p.Ala895Thr) rs201115064 0.00024
NM_007294.4(BRCA1):c.3929C>A (p.Thr1310Lys) rs80357257 0.00024
NM_020975.6(RET):c.874G>A (p.Val292Met) rs34682185 0.00023
NM_024675.4(PALB2):c.656A>G (p.Asp219Gly) rs45594034 0.00021
NM_000051.4(ATM):c.4060C>A (p.Pro1354Thr) rs145119475 0.00019
NM_000059.4(BRCA2):c.5612G>A (p.Ser1871Asn) rs80358782 0.00019
NM_005228.5(EGFR):c.1557G>T (p.Glu519Asp) rs116057045 0.00019
NM_000038.6(APC):c.6637A>G (p.Met2213Val) rs186926737 0.00018
NM_006231.4(POLE):c.1597G>A (p.Val533Met) rs374140892 0.00018
NM_006231.4(POLE):c.6751T>C (p.Phe2251Leu) rs373768478 0.00018
NM_020937.4(FANCM):c.5848T>G (p.Leu1950Val) rs146436929 0.00017
NM_000535.7(PMS2):c.2437C>T (p.Arg813Trp) rs375968016 0.00016
NM_002691.4(POLD1):c.353C>T (p.Ser118Phe) rs780604625 0.00016
NM_006231.4(POLE):c.154C>T (p.Arg52Trp) rs115452881 0.00016
NM_000051.4(ATM):c.2927T>C (p.Val976Ala) rs146145357 0.00014
NM_002907.4(RECQL):c.1465A>G (p.Ile489Val) rs146077019 0.00014
NM_002907.4(RECQL):c.468T>G (p.Ile156Met) rs777214281 0.00013
NM_004360.5(CDH1):c.2635G>A (p.Gly879Ser) rs200911775 0.00013
NM_004656.4(BAP1):c.1408G>A (p.Gly470Arg) rs576538858 0.00012
NM_006231.4(POLE):c.6674G>A (p.Arg2225His) rs538875477 0.00012
NM_020937.4(FANCM):c.5832G>T (p.Leu1944Phe) rs201017015 0.00012
NM_000051.4(ATM):c.5890A>G (p.Lys1964Glu) rs201963507 0.00011
NM_000136.3(FANCC):c.817G>A (p.Glu273Lys) rs143181565 0.00011
NM_000455.5(STK11):c.1038C>T (p.Gly346=) rs767565606 0.00011
NM_002878.4(RAD51D):c.137C>G (p.Ser46Cys) rs587780102 0.00010
NM_006231.4(POLE):c.6531+6G>T rs774747998 0.00010
NM_000051.4(ATM):c.4414T>G (p.Leu1472Val) rs539676759 0.00009
NM_000245.4(MET):c.110T>C (p.Val37Ala) rs201315884 0.00009
NM_000245.4(MET):c.2318C>T (p.Pro773Leu) rs771333219 0.00009
NM_005228.5(EGFR):c.2885G>A (p.Arg962His) rs144496976 0.00009
NM_002907.4(RECQL):c.386G>A (p.Cys129Tyr) rs187203579 0.00008
NM_000051.4(ATM):c.749G>A (p.Arg250Gln) rs56123940 0.00007
NM_000245.4(MET):c.3218C>T (p.Pro1073Leu) rs370529693 0.00007
NM_000249.4(MLH1):c.955G>A (p.Glu319Lys) rs63750796 0.00006
NM_000465.4(BARD1):c.1973G>A (p.Arg658His) rs377227840 0.00006
NM_002878.4(RAD51D):c.715C>T (p.Arg239Trp) rs770250516 0.00006
NM_007194.4(CHEK2):c.1556G>T (p.Arg519Leu) rs587780180 0.00006
NM_024675.4(PALB2):c.1001A>G (p.Tyr334Cys) rs200620434 0.00006
NM_024675.4(PALB2):c.560C>A (p.Pro187His) rs371582757 0.00006
NM_000038.6(APC):c.3625G>A (p.Glu1209Lys) rs201185479 0.00005
NM_000038.6(APC):c.4372C>T (p.Pro1458Ser) rs143796828 0.00005
NM_000136.3(FANCC):c.395C>G (p.Ala132Gly) rs587779905 0.00005
NM_000245.4(MET):c.100G>A (p.Glu34Lys) rs764246939 0.00005
NM_000249.4(MLH1):c.1153C>T (p.Arg385Cys) rs63750760 0.00005
NM_000535.7(PMS2):c.1501G>A (p.Val501Met) rs540287433 0.00004
NM_005228.5(EGFR):c.739G>A (p.Asp247Asn) rs780001754 0.00004
NM_006231.4(POLE):c.4307G>A (p.Arg1436Gln) rs754518522 0.00004
NM_020937.4(FANCM):c.3938G>C (p.Ser1313Thr) rs771311008 0.00004
NM_000038.6(APC):c.647G>A (p.Arg216Gln) rs76685252 0.00003
NM_000051.4(ATM):c.2735A>G (p.Gln912Arg) rs730881353 0.00003
NM_001042492.3(NF1):c.169G>A (p.Gly57Ser) rs779727341 0.00003
NM_005228.5(EGFR):c.345T>A (p.Asn115Lys) rs773596817 0.00003
NM_020937.4(FANCM):c.1667A>G (p.Asp556Gly) rs148810507 0.00003
NM_020975.6(RET):c.3149G>A (p.Arg1050Gln) rs200956659 0.00003
NM_032043.3(BRIP1):c.728T>C (p.Ile243Thr) rs587781860 0.00003
NM_000038.6(APC):c.5308A>G (p.Lys1770Glu) rs551183536 0.00002
NM_000038.6(APC):c.7495G>C (p.Val2499Leu) rs33941929 0.00002
NM_000038.6(APC):c.7550A>G (p.Tyr2517Cys) rs587783036 0.00002
NM_000059.4(BRCA2):c.5270A>G (p.Tyr1757Cys) rs587776466 0.00002
NM_000245.4(MET):c.1640G>A (p.Arg547Gln) rs761951444 0.00002
NM_020975.6(RET):c.1678C>T (p.Pro560Ser) rs748852160 0.00002
NM_022455.5(NSD1):c.6887T>C (p.Val2296Ala) rs754309202 0.00002
NM_000038.6(APC):c.1580G>C (p.Arg527Thr) rs1554081889 0.00001
NM_000038.6(APC):c.2642C>T (p.Ser881Phe) rs535344579 0.00001
NM_000038.6(APC):c.5017G>A (p.Glu1673Lys) rs587779796 0.00001
NM_000051.4(ATM):c.3256C>T (p.Arg1086Cys) rs201780199 0.00001
NM_000059.4(BRCA2):c.7928C>G (p.Ala2643Gly) rs80359018 0.00001
NM_000059.4(BRCA2):c.811G>A (p.Gly271Arg) rs786204274 0.00001
NM_000251.3(MSH2):c.1130A>G (p.Gln377Arg) rs776174711 0.00001
NM_000455.5(STK11):c.559G>A (p.Gly187Ser) rs587782032 0.00001
NM_002691.4(POLD1):c.197C>G (p.Ala66Gly) rs199792522 0.00001
NM_005228.5(EGFR):c.869C>T (p.Thr290Ile) rs1020654485 0.00001
NM_006231.4(POLE):c.4427T>G (p.Phe1476Cys) rs985504177 0.00001
NM_006231.4(POLE):c.5866G>A (p.Glu1956Lys) rs749992643 0.00001
NM_006231.4(POLE):c.6775C>T (p.Arg2259Trp) rs866548835 0.00001
NM_020975.6(RET):c.2166G>T (p.Lys722Asn) rs527726480 0.00001
NM_000038.6(APC):c.4765C>G (p.Arg1589Gly) rs72541813
NM_000038.6(APC):c.7391C>G (p.Ser2464Cys) rs766473931
NM_000057.4(BLM):c.2141C>G (p.Ser714Cys)
NM_000059.4(BRCA2):c.10250A>G (p.Tyr3417Cys) rs730881600
NM_000059.4(BRCA2):c.6095C>T (p.Ala2032Val) rs786202701
NM_000059.4(BRCA2):c.9011A>G (p.Lys3004Arg) rs587782779
NM_000179.3(MSH6):c.1420G>C (p.Val474Leu) rs1558661621
NM_000179.3(MSH6):c.334A>G (p.Asn112Asp) rs864622397
NM_000179.3(MSH6):c.818G>T (p.Gly273Val) rs769610487
NM_000314.8(PTEN):c.-513G>C rs546504608
NM_000314.8(PTEN):c.196A>T (p.Lys66Ter) rs1554897271
NM_000455.5(STK11):c.863-5_863-3del rs764739106
NM_000465.4(BARD1):c.2191C>G (p.Arg731Gly) rs76744638
NM_001040108.2(MLH3):c.149T>A (p.Phe50Tyr) rs148409389
NM_002485.5(NBN):c.832T>G (p.Ser278Ala) rs1225178489
NM_002875.5(RAD51):c.671C>G (p.Ala224Gly)
NM_005228.5(EGFR):c.3245T>G (p.Ile1082Arg) rs1051476261
NM_006231.4(POLE):c.1520T>C (p.Val507Ala) rs904849438
NM_006231.4(POLE):c.2090C>G (p.Pro697Arg) rs36120395
NM_020975.6(RET):c.2342A>G (p.Gln781Arg) rs377767416
NM_022124.6(CDH23):c.6433G>A (p.Val2145Met) rs780523589
NM_024675.4(PALB2):c.1226A>G (p.Tyr409Cys) rs878855097
NM_032043.3(BRIP1):c.3651G>T (p.Trp1217Cys) rs542698396
NM_058216.3(RAD51C):c.1026+5_1026+7del rs587781410
NM_058216.3(RAD51C):c.335G>C (p.Gly112Ala) rs370212314

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