ClinVar Miner

Variants from Vantari Genetics with conflicting interpretations

Location: United States  Primary collection method: clinical testing
Minimum review status of the submission from Vantari Genetics: Collection method of the submission from Vantari Genetics:
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
17 30 0 55 15 0 0 69

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
Vantari Genetics likely pathogenic uncertain significance likely benign benign
pathogenic 2 0 0 0
uncertain significance 0 0 10 9
likely benign 0 1 0 30
benign 0 0 23 0

Submitter to submitter summary #

Total submitters: 13
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
Ambry Genetics 0 51 0 30 14 0 0 44
Sema4, Sema4 0 40 0 18 7 0 0 25
Color Diagnostics, LLC DBA Color Health 0 44 0 15 8 0 0 23
True Health Diagnostics 0 25 0 17 3 0 0 20
Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C. 0 13 0 12 2 0 0 14
Invitae 0 1 0 2 2 0 0 4
Counsyl 0 1 0 1 1 0 0 2
Illumina Laboratory Services, Illumina 0 1 0 2 0 0 0 2
GeneKor MSA 0 2 0 2 0 0 0 2
Fulgent Genetics, Fulgent Genetics 0 0 0 0 1 0 0 1
University of Washington Department of Laboratory Medicine, University of Washington 0 2 0 0 1 0 0 1
Myriad Genetics, Inc. 0 0 0 0 1 0 0 1
Genome-Nilou Lab 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 69
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_002354.3(EPCAM):c.492-5T>C rs78608315 0.02826
NM_000535.7(PMS2):c.1532C>T (p.Thr511Met) rs74902811 0.02492
NM_000051.4(ATM):c.8786+8A>C rs4986839 0.02488
NM_000051.4(ATM):c.5497-8T>C rs3092829 0.02183
NM_000535.7(PMS2):c.1531A>G (p.Thr511Ala) rs2228007 0.02174
NM_024675.4(PALB2):c.2014G>C (p.Glu672Gln) rs45532440 0.02171
NM_024675.4(PALB2):c.629C>T (p.Pro210Leu) rs57605939 0.02101
NM_000059.4(BRCA2):c.5744C>T (p.Thr1915Met) rs4987117 0.01834
NM_024675.4(PALB2):c.2993G>A (p.Gly998Glu) rs45551636 0.01717
NM_000546.6(TP53):c.993+12T>C rs1800899 0.01614
NM_024675.4(PALB2):c.1010T>C (p.Leu337Ser) rs45494092 0.01508
NM_004360.5(CDH1):c.1849G>A (p.Ala617Thr) rs33935154 0.01412
NM_007294.4(BRCA1):c.4956G>A (p.Met1652Ile) rs1799967 0.01348
NM_000051.4(ATM):c.4258C>T (p.Leu1420Phe) rs1800058 0.01150
NM_007294.4(BRCA1):c.2458A>G (p.Lys820Glu) rs56082113 0.00964
NM_000245.4(MET):c.2975C>T (p.Thr992Ile) rs56391007 0.00911
NM_006206.6(PDGFRA):c.236G>A (p.Gly79Asp) rs36035373 0.00897
NM_000051.4(ATM):c.2572T>C (p.Phe858Leu) rs1800056 0.00861
NM_000535.7(PMS2):c.52A>G (p.Ile18Val) rs63750123 0.00861
NM_002485.5(NBN):c.2146A>G (p.Asn716Asp) rs72563785 0.00830
NM_000535.7(PMS2):c.1711C>A (p.Leu571Ile) rs63750055 0.00784
NM_000548.5(TSC2):c.3914C>T (p.Pro1305Leu) rs45517320 0.00758
NM_000051.4(ATM):c.544G>C (p.Val182Leu) rs3218707 0.00757
NM_000059.3(BRCA2):c.5704G>A (p.Asp1902Asn) rs4987048 0.00655
NM_004655.4(AXIN2):c.2282C>A (p.Ala761Asp) rs79732150 0.00649
NM_000059.4(BRCA2):c.4258G>T (p.Asp1420Tyr) rs28897727 0.00609
NM_007294.4(BRCA1):c.5406+8T>C rs55946644 0.00514
NM_000179.3(MSH6):c.457+13A>G rs1800933 0.00434
NM_000245.4(MET):c.504G>T (p.Glu168Asp) rs55985569 0.00420
NM_007294.4(BRCA1):c.4039A>G (p.Arg1347Gly) rs28897689 0.00419
NM_000059.4(BRCA2):c.6347A>G (p.His2116Arg) rs55953736 0.00396
NM_000455.5(STK11):c.1062C>G (p.Phe354Leu) rs59912467 0.00348
NM_001048174.2(MUTYH):c.1103G>A (p.Gly368Asp) rs36053993 0.00341
NM_004360.5(CDH1):c.1774G>A (p.Ala592Thr) rs35187787 0.00311
NM_007294.4(BRCA1):c.557C>A (p.Ser186Tyr) rs55688530 0.00301
NM_024675.4(PALB2):c.2590C>T (p.Pro864Ser) rs45568339 0.00287
NM_000059.4(BRCA2):c.4241C>T (p.Thr1414Met) rs70953664 0.00272
NM_001365951.3(KIF1B):c.3635C>T (p.Pro1212Leu) rs141224290 0.00255
NM_000059.4(BRCA2):c.8182G>A (p.Val2728Ile) rs28897749 0.00239
NM_002691.4(POLD1):c.56G>A (p.Arg19His) rs3218773 0.00197
NM_000051.4(ATM):c.1229T>C (p.Val410Ala) rs56128736 0.00186
NM_004655.4(AXIN2):c.2272G>A (p.Ala758Thr) rs145007501 0.00179
NM_001048174.2(MUTYH):c.1501C>A (p.Leu501Met) rs3219496 0.00154
NM_000251.3(MSH2):c.1387-8G>T rs187525243 0.00143
NM_000059.4(BRCA2):c.8149G>T (p.Ala2717Ser) rs28897747 0.00127
NM_002691.4(POLD1):c.2275G>A (p.Val759Ile) rs145473716 0.00110
NM_000051.4(ATM):c.4388T>G (p.Phe1463Cys) rs138327406 0.00103
NM_005732.4(RAD50):c.1534G>T (p.Ala512Ser) rs147366706 0.00079
NM_005732.4(RAD50):c.3036+5G>A rs181016343 0.00078
NM_005732.4(RAD50):c.671G>A (p.Arg224His) rs28903088 0.00065
NM_004655.4(AXIN2):c.1250C>T (p.Ala417Val) rs201460658 0.00064
NM_007294.4(BRCA1):c.3302G>A (p.Ser1101Asn) rs41293447 0.00064
NM_000245.4(MET):c.71G>A (p.Gly24Glu) rs180985111 0.00055
NM_000059.4(BRCA2):c.7435+6G>A rs81002852 0.00053
NM_000551.4(VHL):c.463+8C>T rs5030834 0.00051
NM_000245.4(MET):c.959C>T (p.Ala320Val) rs35776110 0.00045
NM_001048174.2(MUTYH):c.1174C>A (p.Leu392Met) rs144079536 0.00041
NM_007294.4(BRCA1):c.3708T>G (p.Asn1236Lys) rs28897687 0.00031
NM_000059.4(BRCA2):c.1385A>G (p.Glu462Gly) rs56403624 0.00020
NM_000535.7(PMS2):c.137G>T (p.Ser46Ile) rs121434629 0.00018
NM_007294.4(BRCA1):c.3296C>T (p.Pro1099Leu) rs80357201 0.00016
NM_000245.4(MET):c.1771C>T (p.Arg591Trp) rs45602940 0.00015
NM_000059.4(BRCA2):c.10045A>G (p.Thr3349Ala) rs80358387 0.00010
NM_020975.6(RET):c.1942G>A (p.Val648Ile) rs77711105 0.00007
NM_000179.3(MSH6):c.1844G>C (p.Cys615Ser) rs730881793 0.00005
NM_000059.4(BRCA2):c.3479G>A (p.Arg1160Lys) rs183920365 0.00002
NM_000059.4(BRCA2):c.8850G>T (p.Lys2950Asn) rs28897754
NM_000249.4(MLH1):c.1852_1853delinsGC (p.Lys618Ala) rs35502531
NM_006231.4(POLE):c.2083T>A (p.Phe695Ile) rs5744799

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