ClinVar Miner

Variants from Genome Diagnostics Laboratory,VU University Medical Center Amsterdam with conflicting interpretations

Location: Netherlands — Primary collection method: clinical testing
Minimum review status of the submission from Genome Diagnostics Laboratory,VU University Medical Center Amsterdam: Collection method of the submission from Genome Diagnostics Laboratory,VU University Medical Center Amsterdam:
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
16 217 3 173 54 0 1 199

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 submitters
Genome Diagnostics Laboratory,VU University Medical Center Amsterdam pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 3 5 0 0 0
likely pathogenic 1 0 1 0 0
uncertain significance 0 0 0 2 0
likely benign 0 0 41 0 99
benign 0 0 11 68 0

Submitter to submitter summary #

Total submitters: 30
Download table as spreadsheet
Submitter 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
Illumina Clinical Services Laboratory,Illumina 0 157 0 64 41 0 0 105
DNA and Cytogenetics Diagnostics Unit,Erasmus Medical Center 0 175 0 51 1 0 1 53
Genome Diagnostics Laboratory,University Medical Center Utrecht 0 84 0 47 0 0 0 47
Invitae 0 74 0 41 4 0 0 45
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 122 0 16 0 0 0 16
Mendelics 0 25 0 14 0 0 0 14
Natera, Inc. 0 32 0 9 0 0 0 9
Center for Human Genetics, Inc,Center for Human Genetics, Inc 0 1 0 2 4 0 0 6
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories 0 16 0 5 0 0 0 5
Counsyl 0 18 0 4 1 0 0 5
GeneReviews 0 12 3 2 0 0 0 5
OMIM 0 7 0 1 3 0 0 4
Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) 0 2 0 3 0 0 0 3
Baylor Genetics 0 9 0 1 1 0 0 2
Breast Cancer Information Core (BIC) (BRCA2) 0 0 0 0 2 0 0 2
SIB Swiss Institute of Bioinformatics 0 1 0 2 0 0 0 2
Nilou-Genome Lab 0 1 0 1 1 0 0 2
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics,Children's Hospital of Philadelphia 0 0 0 0 1 0 0 1
Michigan Medical Genetics Laboratories,University of Michigan 0 0 0 1 0 0 0 1
Centre for Inherited Metabolic Diseases, Karolinska University Hospital 0 2 0 1 0 0 0 1
Integrated Genetics/Laboratory Corporation of America 0 5 0 1 0 0 0 1
Fulgent Genetics,Fulgent Genetics 0 6 0 1 0 0 0 1
ClinVar Staff, National Center for Biotechnology Information (NCBI) 0 0 0 1 0 0 0 1
International Society for Gastrointestinal Hereditary Tumours (InSiGHT) 0 0 0 1 0 0 0 1
UCLA Clinical Genomics Center, UCLA 0 0 0 1 0 0 0 1
Knight Diagnostic Laboratories, Oregon Health and Sciences University 0 2 0 0 1 0 0 1
Neurogenetics Laboratory,GH Pitie Salpetriere APHP 0 0 0 1 0 0 0 1
Soonchunhyang University Bucheon Hospital,Soonchunhyang University Medical Center 0 0 0 0 1 0 0 1
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago 0 0 0 0 1 0 0 1
Myriad Women's Health, Inc. 0 3 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 199
Download table as spreadsheet
HGVS dbSNP
NM_000020.2(ACVRL1):c.207C>T (p.Cys69=) rs56080682
NM_000020.3(ACVRL1):c.1445C>T (p.Ala482Val) rs139142865
NM_000043.6(FAS):c.46G>A (p.Ala16Thr) rs3218619
NM_000043.6(FAS):c.578A>G (p.Lys193Arg) rs150489856
NM_000051.3(ATM):c.1236-3del rs34325032
NM_000051.3(ATM):c.162T>C (p.Tyr54=) rs3218690
NM_000051.3(ATM):c.2119T>C (p.Ser707Pro) rs4986761
NM_000051.3(ATM):c.2572T>C (p.Phe858Leu) rs1800056
NM_000051.3(ATM):c.3403-15T>A rs79701258
NM_000051.3(ATM):c.4258C>T (p.Leu1420Phe) rs1800058
NM_000051.3(ATM):c.4324T>C (p.Tyr1442His) rs201666889
NM_000051.3(ATM):c.4473C>T (p.Phe1491=) rs4988008
NM_000051.3(ATM):c.544G>C (p.Val182Leu) rs3218707
NM_000051.3(ATM):c.5497-8T>C rs3092829
NM_000051.3(ATM):c.5558A>T (p.Asp1853Val) rs1801673
NM_000051.3(ATM):c.6235G>A (p.Val2079Ile) rs1800060
NM_000051.3(ATM):c.6347+31del rs58978479
NM_000051.3(ATM):c.735C>T (p.Val245=) rs3218674
NM_000051.3(ATM):c.8786+8A>C rs4986839
NM_000051.4(ATM):c.1066-6T>G rs201686625
NM_000051.4(ATM):c.146C>G rs1800054
NM_000051.4(ATM):c.1810C>T (p.Pro604Ser) rs2227922
NM_000051.4(ATM):c.3925G>A (p.Ala1309Thr) rs149711770
NM_000051.4(ATM):c.5071A>C (p.Ser1691Arg) rs1800059
NM_000059.3(BRCA2):c.1040A>G (p.Gln347Arg) rs55800493
NM_000059.3(BRCA2):c.1911T>C (p.Gly637=) rs11571652
NM_000059.3(BRCA2):c.4584C>T (p.Ser1528=) rs80359788
NM_000071.3(CBS):c.531+11G>A rs186114513
NM_000123.3(ERCC5):c.1110T>A (p.Arg370=) rs150791877
NM_000123.3(ERCC5):c.1789G>C (p.Val597Leu) rs4150319
NM_000123.3(ERCC5):c.2353C>T (p.Gln785Ter) rs1244074570
NM_000123.3(ERCC5):c.2818G>A (p.Val940Met) rs146344855
NM_000123.3(ERCC5):c.767A>G (p.Gln256Arg) rs4150313
NM_000123.3(ERCC5):c.960C>T (p.Asp320=) rs4150314
NM_000135.4(FANCA):c.1573A>G (p.Ile525Val) rs755925068
NM_000135.4(FANCA):c.3859G>A (p.Val1287Ile) rs17227354
NM_000179.2(MSH6):c.1186C>G (p.Leu396Val) rs2020908
NM_000179.2(MSH6):c.1449G>T (p.Val483=) rs35590297
NM_000179.2(MSH6):c.2633T>C (p.Val878Ala) rs2020912
NM_000179.2(MSH6):c.457+13A>G rs1800933
NM_000179.3(MSH6):c.3246G>T (p.Pro1082=) rs3136351
NM_000179.3(MSH6):c.431G>T (p.Ser144Ile) rs3211299
NM_000249.4(MLH1):c.1959G>T (p.Leu653=) rs1800146
NM_000249.4(MLH1):c.2152C>T (p.His718Tyr) rs2020873
NM_000251.2(MSH2):c.1077-10T>C rs17224360
NM_000251.2(MSH2):c.1387-8G>T rs187525243
NM_000251.2(MSH2):c.1662-9G>A rs17218356
NM_000251.2(MSH2):c.1666T>C (p.Leu556=) rs61756466
NM_000251.2(MSH2):c.1886A>G (p.Gln629Arg) rs61756468
NM_000251.2(MSH2):c.573C>T (p.Leu191=) rs1800151
NM_000251.2(MSH2):c.965G>A (p.Gly322Asp) rs4987188
NM_000251.3(MSH2):c.339G>A (p.Lys113=) rs35898375
NM_000251.3(MSH2):c.380A>G (p.Asn127Ser) rs17217772
NM_000251.3(MSH2):c.471C>A (p.Gly157=) rs61756463
NM_000271.5(NPC1):c.1503C>T (p.Asp501=) rs116046557
NM_000271.5(NPC1):c.1532C>T (p.Thr511Met) rs13381670
NM_000271.5(NPC1):c.1947+14G>T rs3745024
NM_000271.5(NPC1):c.1947+8_1947+10dup rs3837910
NM_000271.5(NPC1):c.1947+8_1947+11dup rs3837910
NM_000271.5(NPC1):c.1947+8dup rs3837910
NM_000271.5(NPC1):c.2073G>A (p.Pro691=) rs113013085
NM_000271.5(NPC1):c.2795+19T>C rs200103695
NM_000271.5(NPC1):c.3019C>G (p.Pro1007Ala) rs80358257
NM_000271.5(NPC1):c.3198C>T (p.Thr1066=) rs145145840
NM_000271.5(NPC1):c.3450C>T (p.Asn1150=) rs34715591
NM_000271.5(NPC1):c.3477+19T>C rs375942184
NM_000271.5(NPC1):c.3561G>T (p.Ala1187=) rs55724504
NM_000271.5(NPC1):c.540C>T (p.Asp180=) rs143656971
NM_000271.5(NPC1):c.665A>G (p.Asn222Ser) rs55680026
NM_000271.5(NPC1):c.709C>T (p.Pro237Ser) rs80358251
NM_000303.3(PMM2):c.357C>A (p.Phe119Leu) rs80338701
NM_000303.3(PMM2):c.422G>A (p.Arg141His) rs28936415
NM_000360.4(TH):c.1200+9C>T rs11564717
NM_000360.4(TH):c.267G>A (p.Arg89=) rs76240471
NM_000535.7(PMS2):c.1266G>A (p.Glu422=) rs138049175
NM_000535.7(PMS2):c.1437C>G (p.His479Gln) rs63750685
NM_000535.7(PMS2):c.1488C>T (p.His496=) rs1805320
NM_000535.7(PMS2):c.1531A>G (p.Thr511Ala) rs2228007
NM_000535.7(PMS2):c.1532C>T (p.Thr511Met) rs74902811
NM_000535.7(PMS2):c.1688G>T (p.Arg563Leu) rs63750668
NM_000535.7(PMS2):c.1789A>T (p.Thr597Ser) rs1805318
NM_000535.7(PMS2):c.1866G>A (p.Met622Ile) rs1805324
NM_000535.7(PMS2):c.23+10G>C rs192027828
NM_000535.7(PMS2):c.52A>G (p.Ile18Val) rs63750123
NM_000535.7(PMS2):c.706-20dup rs60794673
NM_000535.7(PMS2):c.706-4del rs60794673
NM_001044.5(SLC6A3):c.114C>T (p.Asn38=) rs6350
NM_001044.5(SLC6A3):c.546C>T (p.Asn182=) rs28364996
NM_001103146.3(GIGYF2):c.3629_3630insGC (p.Gln1211fs) rs371622656
NM_001167617.2(MLH1):c.1852G>A (p.Val618Met) rs35831931
NM_001182.5(ALDH7A1):c.1279G>C (p.Glu427Gln) rs121912707
NM_001257180.2(SLC20A2):c.1008C>T (p.His336=) rs111553899
NM_001257180.2(SLC20A2):c.1011C>A (p.Thr337=) rs116359869
NM_001257180.2(SLC20A2):c.1254C>T (p.Gly418=) rs115234947
NM_001257180.2(SLC20A2):c.1438G>A (p.Ala480Thr) rs79577461
NM_001257180.2(SLC20A2):c.1812C>T (p.Ala604=) rs116401889
NM_001257180.2(SLC20A2):c.345G>A (p.Thr115=) rs34124953
NM_001257180.2(SLC20A2):c.58T>C (p.Leu20=) rs115993270
NM_001257180.2(SLC20A2):c.909G>A (p.Ala303=) rs75248974
NM_001367624.1(ZNF469):c.457C>G (p.Pro153Ala) rs532620482
NM_001909.5(CTSD):c.1072-7G>A rs149019571
NM_001909.5(CTSD):c.1215C>A (p.Gly405=) rs138733377
NM_001909.5(CTSD):c.173C>T (p.Ala58Val) rs17571
NM_001909.5(CTSD):c.189C>T (p.Thr63=) rs114051835
NM_001909.5(CTSD):c.353-12C>T rs141523461
NM_001909.5(CTSD):c.639C>G (p.Pro213=) rs146073498
NM_001909.5(CTSD):c.827+13T>C rs369602025
NM_001909.5(CTSD):c.844G>A (p.Gly282Arg) rs147278302
NM_001999.4(FBN2):c.110C>A (p.Pro37Gln) rs201255083
NM_001999.4(FBN2):c.2427T>A (p.Ile809=) rs139686090
NM_001999.4(FBN2):c.2940C>T (p.Cys980=) rs143255082
NM_001999.4(FBN2):c.5448A>G (p.Pro1816=) rs138022198
NM_001999.4(FBN2):c.5674+7A>G rs367877964
NM_001999.4(FBN2):c.7380C>T (p.Cys2460=) rs147102633
NM_001999.4(FBN2):c.8304C>T (p.Asn2768=) rs28763920
NM_001999.4(FBN2):c.8364+7A>T rs185052980
NM_001999.4(FBN2):c.953-8T>G rs201818403
NM_001999.4(FBN2):c.976C>T (p.Pro326Ser) rs28763954
NM_002474.3(MYH11):c.12G>A (p.Lys4=) rs112650390
NM_002474.3(MYH11):c.2049C>T (p.His683=) rs150924100
NM_002474.3(MYH11):c.2520+17A>G rs185697714
NM_002474.3(MYH11):c.2893G>T (p.Ala965Ser) rs113696032
NM_002474.3(MYH11):c.300C>T (p.Ser100=) rs111662326
NM_002474.3(MYH11):c.3652-6C>T rs193922630
NM_002474.3(MYH11):c.3828G>A (p.Ala1276=) rs113154524
NM_002474.3(MYH11):c.4158C>T (p.Thr1386=) rs112377790
NM_002474.3(MYH11):c.4522A>G (p.Met1508Val) rs35176378
NM_002474.3(MYH11):c.453G>A (p.Pro151=) rs61734199
NM_002474.3(MYH11):c.4578+3A>G rs143288748
NM_002474.3(MYH11):c.5566C>T (p.Leu1856=) rs142639688
NM_002474.3(MYH11):c.5614-7G>A rs202120792
NM_002474.3(MYH11):c.739C>T (p.Arg247Cys) rs150759461
NM_002474.3(MYH11):c.792T>C (p.Tyr264=) rs34341838
NM_002474.3(MYH11):c.987C>T (p.Thr329=) rs4781689
NM_002608.4(PDGFB):c.635C>T (p.Thr212Met) rs114786489
NM_003332.3(TYROBP):c.94+10G>C rs55746266
NM_003900.5(SQSTM1):c.822G>C (p.Glu274Asp) rs55793208
NM_003900.5(SQSTM1):c.954C>T (p.Ser318=) rs56092424
NM_004064.4(CDKN1B):c.426G>A (p.Thr142=) rs149775942
NM_004181.5(UCHL1):c.53C>A (p.Ser18Tyr) rs5030732
NM_004304.5(ALK):c.2039C>T (p.Thr680Ile) rs35228363
NM_004304.5(ALK):c.3594C>T (p.Leu1198=) rs56071005
NM_004304.5(ALK):c.4785C>T (p.Ala1595=) rs76150405
NM_004385.5(VCAN):c.1523T>A (p.Ile508Asn) rs143368552
NM_004385.5(VCAN):c.7419C>T (p.Ser2473=) rs61754536
NM_005211.3(CSF1R):c.2760G>C (p.Glu920Asp) rs34030164
NM_005211.3(CSF1R):c.282C>T (p.Ser94=) rs41287102
NM_005211.3(CSF1R):c.294C>T (p.His98=) rs17652007
NM_005590.4(MRE11):c.120C>T (p.Leu40=) rs1805364
NM_005591.3(MRE11):c.315-4del rs35062043
NM_006502.2(POLH):c.626G>T (p.Gly209Val) rs2307456
NM_007255.3(B4GALT7):c.411C>T (p.Phe137=) rs142951817
NM_007294.4(BRCA1):c.2814A>G (p.Pro938=) rs80356851
NM_007375.3(TARDBP):c.198T>C (p.Ala66=) rs61730366
NM_012179.4(FBXO7):c.122+9G>A rs192327462
NM_012179.4(FBXO7):c.540A>G (p.Pro180=) rs41311141
NM_013254.4(TBK1):c.1391T>C (p.Val464Ala) rs35635889
NM_014317.5(PDSS1):c.589A>G (p.Lys197Glu) rs116424900
NM_014946.4(SPAST):c.1496G>A rs878854991
NM_015575.4(GIGYF2):c.1554G>A (p.Glu518=) rs2305138
NM_016038.4(SBDS):c.635T>C (p.Ile212Thr) rs79344818
NM_016938.5(EFEMP2):c.1188C>T (p.Ser396=) rs2234473
NM_016938.5(EFEMP2):c.277G>A (p.Gly93Ser) rs2234462
NM_016938.5(EFEMP2):c.368-4G>A rs111550973
NM_016938.5(EFEMP2):c.885C>T (p.Ser295=) rs142509316
NM_018026.4(PACS1):c.607C>T (p.Arg203Trp) rs398123009
NM_018082.5(POLR3B):c.1568T>A rs138249161
NM_018965.3(TREM2):c.185G>A (p.Arg62His) rs143332484
NM_021076.4(NEFH):c.1947_1964dup (p.646_651AKSPEK[3]) rs147489453
NM_024306.5(FA2H):c.289C>G (p.Pro97Ala) rs35874850
NM_024649.5(BBS1):c.24T>C (p.Asp8=) rs55848325
NM_025137.4(SPG11):c.1108G>A (p.Glu370Lys) rs77697105
NM_025137.4(SPG11):c.1698T>G (p.Asp566Glu) rs79708848
NM_025137.4(SPG11):c.176C>T (p.Ala59Val) rs552320263
NM_025137.4(SPG11):c.2083G>A (p.Ala695Thr) rs78183930
NM_025137.4(SPG11):c.257+13G>A rs201936649
NM_025137.4(SPG11):c.3818A>G (p.Lys1273Arg) rs76389165
NM_025137.4(SPG11):c.6224A>G (p.Asn2075Ser) rs140824939
NM_025137.4(SPG11):c.6258G>T (p.Leu2086=) rs150761878
NM_025137.4(SPG11):c.6319G>A (p.Val2107Ile) rs115970214
NM_025137.4(SPG11):c.7023C>T (p.Tyr2341=) rs80338869
NM_025137.4(SPG11):c.7256A>G (p.Lys2419Arg) rs76116949
NM_025137.4(SPG11):c.808G>A (p.Val270Ile) rs80338868
NM_030582.4(COL18A1):c.3321C>T (p.Pro1107=) rs11544970
NM_030777.4(SLC2A10):c.1512G>A (p.Ser504=) rs117587497
NM_030777.4(SLC2A10):c.330C>T (p.Phe110=) rs199848479
NM_030777.4(SLC2A10):c.515C>T (p.Thr172Ile) rs143301610
NM_030777.4(SLC2A10):c.816C>G (p.Ala272=) rs148058006
NM_031885.4(BBS2):c.1413A>C (p.Val471=) rs35294865
NM_031885.4(BBS2):c.1422G>A (p.Ser474=) rs117033008
NM_031885.4(BBS2):c.805-20A>G rs41280892
NM_152490.5(B3GALNT2):c.824_825dup (p.Ile276fs) rs367543075
NM_152618.3(BBS12):c.116T>C (p.Ile39Thr) rs138036823
NM_152618.3(BBS12):c.714T>G (p.Asn238Lys) rs17006082
NM_176824.3(BBS7):c.1512-7A>T rs115987385
NM_182895.5(SCARF2):c.1967C>T (p.Pro656Leu) rs9680797
NM_198428.3(BBS9):c.1648A>G (p.Ile550Val) rs150399299
NM_198428.3(BBS9):c.2299-20A>C rs17727583
NM_198428.3(BBS9):c.2632+9C>A rs148654647

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