ClinVar Miner

Variants with conflicting interpretations between GeneDx and Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute

Minimum review status of the submission from GeneDx: Collection method of the submission from GeneDx:
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
6 465 0 140 27 0 4 171

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.

pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 4 1 0 0
likely pathogenic 3 0 2 0 0
uncertain significance 0 1 0 20 2
likely benign 0 0 5 0 49
benign 0 0 0 84 0

All variants with conflicting interpretations #

Total variants: 171
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_024675.4(PALB2):c.212-58A>C rs80291632 0.02171
NM_000051.4(ATM):c.2125-68T>C rs2235008 0.01573
NM_002878.4(RAD51D):c.903+53C>T rs45496096 0.01225
NM_000051.4(ATM):c.3993+40G>A rs3218709 0.00933
NM_000546.6(TP53):c.1100+30A>T rs17880847 0.00929
NM_000249.4(MLH1):c.1732-19T>A rs77120160 0.00923
NM_000051.4(ATM):c.8419-19A>G rs12279930 0.00824
NM_000051.4(ATM):c.2119T>C (p.Ser707Pro) rs4986761 0.00782
NM_000059.4(BRCA2):c.316+108A>G rs115376548 0.00769
NM_000059.4(BRCA2):c.8632+132dup rs201392123 0.00742
NM_058216.3(RAD51C):c.859A>G (p.Thr287Ala) rs28363317 0.00653
NM_000051.4(ATM):c.5793T>C (p.Ala1931=) rs3092910 0.00608
NM_000051.4(ATM):c.4042T>C (p.Leu1348=) rs56355831 0.00599
NM_058216.3(RAD51C):c.572-17G>T rs193023469 0.00513
NM_007294.4(BRCA1):c.-192T>C rs113323025 0.00510
NM_000051.4(ATM):c.5558A>T (p.Asp1853Val) rs1801673 0.00441
NM_000051.4(ATM):c.1810C>T (p.Pro604Ser) rs2227922 0.00431
NM_000179.3(MSH6):c.1345C>T (p.Leu449=) rs3136333 0.00429
NM_000051.4(ATM):c.5762+27G>A rs3218686 0.00428
NM_000051.4(ATM):c.2250+22A>C rs3218692 0.00419
NM_000249.4(MLH1):c.453+25A>G rs4647246 0.00414
NM_000249.4(MLH1):c.307-29C>A rs139620056 0.00398
NM_000051.4(ATM):c.5497-15G>C rs3092828 0.00363
NM_058216.3(RAD51C):c.376G>A (p.Ala126Thr) rs61758784 0.00349
NM_024675.4(PALB2):c.1572A>G (p.Ser524=) rs45472400 0.00312
NM_024675.4(PALB2):c.2590C>T (p.Pro864Ser) rs45568339 0.00287
NM_032043.3(BRIP1):c.2097+7G>A rs4988352 0.00271
NM_058216.3(RAD51C):c.790G>A (p.Gly264Ser) rs147241704 0.00207
NM_007194.4(CHEK2):c.254C>T (p.Pro85Leu) rs17883862 0.00201
NM_032043.3(BRIP1):c.584T>C (p.Leu195Pro) rs4988347 0.00197
NM_000051.4(ATM):c.8269-14A>T rs114320959 0.00195
NM_024675.4(PALB2):c.1606C>T (p.Leu536=) rs151162255 0.00193
NM_024675.4(PALB2):c.2256A>G (p.Gly752=) rs147120218 0.00193
NM_000535.7(PMS2):c.23+10G>C rs192027828 0.00182
NM_000059.4(BRCA2):c.4187A>G (p.Gln1396Arg) rs55969723 0.00168
NM_000051.4(ATM):c.7788+8G>T rs112775908 0.00165
NM_024675.4(PALB2):c.2742C>T (p.Phe914=) rs115759702 0.00143
NM_000251.3(MSH2):c.1737A>G (p.Lys579=) rs61756467 0.00138
NM_000051.4(ATM):c.998C>T (p.Ser333Phe) rs28904919 0.00137
NM_000059.4(BRCA2):c.6821G>T (p.Gly2274Val) rs55712212 0.00126
NM_000051.4(ATM):c.4473C>T (p.Phe1491=) rs4988008 0.00125
NM_024675.4(PALB2):c.2816T>G (p.Leu939Trp) rs45478192 0.00121
NM_024675.4(PALB2):c.3495G>A (p.Ser1165=) rs45439097 0.00121
NM_000059.4(BRCA2):c.1040A>G (p.Gln347Arg) rs55800493 0.00109
NM_000059.4(BRCA2):c.1911T>C (p.Gly637=) rs11571652 0.00109
NM_024675.4(PALB2):c.1194G>A (p.Val398=) rs61755173 0.00103
NM_000059.4(BRCA2):c.6057C>T (p.Asn2019=) rs147961615 0.00102
NM_024675.4(PALB2):c.2365C>T (p.Leu789=) rs145805054 0.00099
NM_000059.4(BRCA2):c.1514T>C (p.Ile505Thr) rs28897708 0.00074
NM_024675.4(PALB2):c.2996+17T>C rs180177128 0.00060
NM_000051.4(ATM):c.8592C>T (p.Tyr2864=) rs56025670 0.00051
NM_000059.4(BRCA2):c.7544C>T (p.Thr2515Ile) rs28897744 0.00048
NM_000051.4(ATM):c.1986T>C (p.Phe662=) rs1800055 0.00046
NM_000051.4(ATM):c.4709T>C (p.Val1570Ala) rs140856217 0.00046
NM_000059.4(BRCA2):c.7976+45G>C rs11571718 0.00046
NM_000059.4(BRCA2):c.4585G>A (p.Gly1529Arg) rs28897728 0.00044
NM_000251.3(MSH2):c.1680T>C (p.Asn560=) rs200056411 0.00043
NM_007294.4(BRCA1):c.-20+11C>T rs273898672 0.00042
NM_007194.4(CHEK2):c.*18C>T rs17884403 0.00037
NM_007194.4(CHEK2):c.1312G>T (p.Asp438Tyr) rs200050883 0.00034
NM_032043.3(BRIP1):c.380-17T>A rs200050729 0.00034
NM_007194.4(CHEK2):c.1427C>T (p.Thr476Met) rs142763740 0.00032
NM_000059.4(BRCA2):c.1395A>C (p.Val465=) rs11571641 0.00026
NM_000059.4(BRCA2):c.4686A>G (p.Gln1562=) rs28897730 0.00026
NM_000059.4(BRCA2):c.9292T>C (p.Tyr3098His) rs41293521 0.00026
NM_007194.4(CHEK2):c.444+19T>C rs200501745 0.00026
NM_000059.4(BRCA2):c.1786G>C (p.Asp596His) rs56328701 0.00025
NM_058216.3(RAD51C):c.145+12T>G rs377297129 0.00024
NM_000059.4(BRCA2):c.5070A>C (p.Lys1690Asn) rs56087561 0.00023
NM_000059.4(BRCA2):c.1385A>G (p.Glu462Gly) rs56403624 0.00020
NM_000051.4(ATM):c.1272T>C (p.Pro424=) rs35578748 0.00019
NM_000051.4(ATM):c.4980C>T (p.Asn1660=) rs144338238 0.00019
NM_000059.4(BRCA2):c.7805+13A>G rs149769332 0.00019
NM_000059.4(BRCA2):c.8905G>A (p.Val2969Met) rs59004709 0.00019
NM_007294.4(BRCA1):c.4484+14A>G rs80358022 0.00019
NM_000249.4(MLH1):c.1040C>A (p.Thr347Asn) rs201541505 0.00017
NM_007194.4(CHEK2):c.1489G>A (p.Asp497Asn) rs143965148 0.00014
NM_032043.3(BRIP1):c.-30-3T>C rs370728413 0.00014
NM_000051.4(ATM):c.1773T>C (p.Asn591=) rs61734356 0.00013
NM_000059.4(BRCA2):c.2919G>A (p.Ser973=) rs45525041 0.00012
NM_000059.4(BRCA2):c.3055C>G (p.Leu1019Val) rs55638633 0.00012
NM_000059.4(BRCA2):c.2680G>A (p.Val894Ile) rs28897715 0.00011
NM_000059.4(BRCA2):c.943T>A (p.Cys315Ser) rs79483201 0.00011
NM_007294.4(BRCA1):c.1065G>A (p.Lys355=) rs41286292 0.00011
NM_032043.3(BRIP1):c.3444C>A (p.Asp1148Glu) rs28997573 0.00011
NM_005359.6(SMAD4):c.21G>A (p.Thr7=) rs142292491 0.00010
NM_000051.4(ATM):c.4414T>G (p.Leu1472Val) rs539676759 0.00009
NM_000059.4(BRCA2):c.2538A>C (p.Ser846=) rs11571654 0.00009
NM_000059.4(BRCA2):c.4614T>C (p.Ser1538=) rs45520945 0.00009
NM_000059.4(BRCA2):c.516+18T>C rs81002834 0.00009
NM_000546.6(TP53):c.6G>A (p.Glu2=) rs143458271 0.00009
NM_001048174.2(MUTYH):c.612C>T (p.Thr204=) rs780747266 0.00009
NM_007194.4(CHEK2):c.349A>G (p.Arg117Gly) rs28909982 0.00009
NM_007294.4(BRCA1):c.2352G>A (p.Ser784=) rs372017932 0.00009
NM_007294.4(BRCA1):c.5152+20T>A rs376836050 0.00009
NM_000059.4(BRCA2):c.6748A>G (p.Thr2250Ala) rs80358899 0.00008
NM_000059.4(BRCA2):c.9501+3A>T rs61757642 0.00008
NM_000455.5(STK11):c.598-7G>A rs377502057 0.00008
NM_000051.4(ATM):c.2021A>G (p.His674Arg) rs201762714 0.00007
NM_007294.4(BRCA1):c.1865C>T (p.Ala622Val) rs56039126 0.00007
NM_000051.4(ATM):c.7521C>T (p.Asp2507=) rs751234924 0.00006
NM_000059.4(BRCA2):c.1011C>T (p.Asn337=) rs41293473 0.00006
NM_000059.4(BRCA2):c.7050C>T (p.Thr2350=) rs587780870 0.00006
NM_000059.4(BRCA2):c.7057G>C (p.Gly2353Arg) rs80358935 0.00006
NM_000059.4(BRCA2):c.8662C>T (p.Arg2888Cys) rs80359123 0.00006
NM_007194.4(CHEK2):c.1260-10C>G rs730881706 0.00006
NM_007294.4(BRCA1):c.1617G>A (p.Thr539=) rs372002119 0.00006
NM_007294.4(BRCA1):c.2412G>C (p.Gln804His) rs55746541 0.00006
NM_007294.4(BRCA1):c.5278-14C>G rs80358105 0.00006
NM_000059.4(BRCA2):c.5268A>G (p.Val1756=) rs199879914 0.00005
NM_000059.4(BRCA2):c.8525G>A (p.Arg2842His) rs80359105 0.00005
NM_007294.4(BRCA1):c.5117G>C (p.Gly1706Ala) rs80356860 0.00005
NM_000059.4(BRCA2):c.4570T>G (p.Phe1524Val) rs56386506 0.00004
NM_000059.4(BRCA2):c.6143A>T (p.Asn2048Ile) rs80358853 0.00004
NM_000059.4(BRCA2):c.7010C>T (p.Thr2337Ile) rs80358927 0.00004
NM_007294.4(BRCA1):c.288C>T (p.Asp96=) rs146085503 0.00004
NM_007294.4(BRCA1):c.976G>C (p.Glu326Gln) rs773433679 0.00004
NM_000059.4(BRCA2):c.3581G>A (p.Gly1194Asp) rs28897721 0.00003
NM_000059.4(BRCA2):c.3682A>G (p.Asn1228Asp) rs28897722 0.00003
NM_000059.4(BRCA2):c.8134G>A (p.Asp2712Asn) rs80359056 0.00003
NM_000059.4(BRCA2):c.8421G>A (p.Ser2807=) rs371278843 0.00003
NM_000059.4(BRCA2):c.8694G>A (p.Leu2898=) rs556762256 0.00003
NM_007294.4(BRCA1):c.396C>A (p.Asn132Lys) rs80357413 0.00003
NM_000051.4(ATM):c.2159G>A (p.Arg720His) rs55830714 0.00002
NM_000051.4(ATM):c.4201T>A (p.Leu1401Ile) rs587779838 0.00002
NM_000051.4(ATM):c.8671+18T>C rs763189977 0.00002
NM_000059.4(BRCA2):c.1804G>A (p.Gly602Arg) rs80358466 0.00002
NM_000059.4(BRCA2):c.5688A>G (p.Ala1896=) rs768907899 0.00002
NM_000059.4(BRCA2):c.7507G>A (p.Val2503Ile) rs587782191 0.00002
NM_000059.4(BRCA2):c.794-11T>C rs81002822 0.00002
NM_007294.4(BRCA1):c.5074+6C>G rs80358032 0.00002
NM_007294.4(BRCA1):c.5334T>C (p.Asp1778=) rs754152768 0.00002
NM_000059.4(BRCA2):c.10023C>T (p.Asp3341=) rs113507014 0.00001
NM_000059.4(BRCA2):c.2416G>C (p.Asp806His) rs56404215 0.00001
NM_000059.4(BRCA2):c.5390C>G (p.Ala1797Gly) rs80358760 0.00001
NM_000059.4(BRCA2):c.5427C>T (p.Cys1809=) rs80359791 0.00001
NM_000059.4(BRCA2):c.68-17A>G rs1060504621 0.00001
NM_000059.4(BRCA2):c.7090G>A (p.Glu2364Lys) rs80358940 0.00001
NM_000059.4(BRCA2):c.7463G>A (p.Arg2488Lys) rs80358968 0.00001
NM_000059.4(BRCA2):c.8417C>T (p.Ser2806Leu) rs587782785 0.00001
NM_000059.4(BRCA2):c.8668C>A (p.Leu2890Ile) rs80359127 0.00001
NM_000059.4(BRCA2):c.9371A>T (p.Asn3124Ile) rs28897759 0.00001
NM_007194.4(CHEK2):c.1036C>T (p.Arg346Cys) rs201206424 0.00001
NM_007194.4(CHEK2):c.1420C>T (p.Arg474Cys) rs540635787 0.00001
NM_007294.4(BRCA1):c.2613G>A (p.Pro871=) rs587782608 0.00001
NM_024675.4(PALB2):c.1697G>A (p.Arg566His) rs144617793 0.00001
NM_024675.4(PALB2):c.3113+5G>C rs876659463 0.00001
NM_000051.4(ATM):c.2922-8del rs373881770
NM_000051.4(ATM):c.331+5G>A rs752135143
NM_000051.4(ATM):c.6198+130G>A rs55982799
NM_000051.4(ATM):c.9019G>T (p.Glu3007Ter) rs876660382
NM_000059.4(BRCA2):c.1355T>C (p.Leu452Pro) rs753512842
NM_000059.4(BRCA2):c.1860T>G (p.Phe620Leu) rs1064793402
NM_000059.4(BRCA2):c.2803G>C (p.Asp935His) rs28897716
NM_000059.4(BRCA2):c.5117A>C (p.Asn1706Thr) rs730881536
NM_000059.4(BRCA2):c.68-7dup rs276174878
NM_000059.4(BRCA2):c.7370T>G (p.Phe2457Cys) rs876661273
NM_000059.4(BRCA2):c.8754+3G>C rs397508007
NM_000059.4(BRCA2):c.9116C>T (p.Pro3039Leu) rs80359167
NM_000264.5(PTCH1):c.-24GGC[8] rs71366293
NM_000314.8(PTEN):c.802-3del rs34003473
NM_000535.7(PMS2):c.1688G>T (p.Arg563Leu) rs63750668
NM_001042492.3(NF1):c.730+32del rs71142032
NM_002382.5(MAX):c.37-15del rs747340873
NM_007294.4(BRCA1):c.302-41T>C rs8176135
NM_007294.4(BRCA1):c.3952A>G (p.Ile1318Val) rs397509121
NM_007294.4(BRCA1):c.4484G>A (p.Arg1495Lys) rs80357389
NM_007294.4(BRCA1):c.5089T>C (p.Cys1697Arg) rs80356993
NM_007294.4(BRCA1):c.5152+85del rs8176259
NM_007294.4(BRCA1):c.547+14del rs273902771
NM_024675.4(PALB2):c.2607C>T (p.Ser869=) rs45542234

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