ClinVar Miner

Variants with conflicting interpretations between ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories and Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute

Minimum review status of the submission from ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories: Collection method of the submission from ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories:
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
4 344 0 58 7 0 1 66

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 uncertain significance likely benign benign
likely pathogenic 1 1 0 0
uncertain significance 0 0 6 1
likely benign 0 0 0 13
benign 0 0 44 0

All variants with conflicting interpretations #

Total variants: 66
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000051.4(ATM):c.8419-19A>G rs12279930 0.00824
NM_000051.4(ATM):c.2119T>C (p.Ser707Pro) rs4986761 0.00782
NM_000051.4(ATM):c.3383A>G (p.Gln1128Arg) rs2229020 0.00636
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_000051.4(ATM):c.1810C>T (p.Pro604Ser) rs2227922 0.00431
NM_000179.3(MSH6):c.1345C>T (p.Leu449=) rs3136333 0.00429
NM_000038.6(APC):c.933+30A>G rs145211300 0.00412
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_032043.3(BRIP1):c.577G>A (p.Val193Ile) rs4988346 0.00305
NM_024675.4(PALB2):c.2590C>T (p.Pro864Ser) rs45568339 0.00287
NM_032043.3(BRIP1):c.2097+7G>A rs4988352 0.00271
NM_000059.4(BRCA2):c.8503T>C (p.Ser2835Pro) rs11571746 0.00202
NM_007194.4(CHEK2):c.254C>T (p.Pro85Leu) rs17883862 0.00201
NM_000051.4(ATM):c.8269-14A>T rs114320959 0.00195
NM_000535.7(PMS2):c.23+10G>C rs192027828 0.00182
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_000051.4(ATM):c.4473C>T (p.Phe1491=) rs4988008 0.00125
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_000059.4(BRCA2):c.6057C>T (p.Asn2019=) rs147961615 0.00102
NM_024675.4(PALB2):c.2365C>T (p.Leu789=) rs145805054 0.00099
NM_000051.4(ATM):c.3925G>A (p.Ala1309Thr) rs149711770 0.00081
NM_007294.4(BRCA1):c.2733A>G (p.Gly911=) rs1800740 0.00066
NM_007294.4(BRCA1):c.981A>G (p.Thr327=) rs1800063 0.00065
NM_032043.3(BRIP1):c.430G>A (p.Ala144Thr) rs116952709 0.00055
NM_000051.4(ATM):c.6919C>T (p.Leu2307Phe) rs56009889 0.00035
NM_007194.4(CHEK2):c.1427C>T (p.Thr476Met) rs142763740 0.00032
NM_007294.4(BRCA1):c.3708T>G (p.Asn1236Lys) rs28897687 0.00031
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_000059.4(BRCA2):c.6322C>T (p.Arg2108Cys) rs55794205 0.00019
NM_007294.4(BRCA1):c.4484+14A>G rs80358022 0.00019
NM_007294.4(BRCA1):c.5406+33A>T rs80358092 0.00018
NM_000059.4(BRCA2):c.2919G>A (p.Ser973=) rs45525041 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_032043.3(BRIP1):c.3444C>A (p.Asp1148Glu) rs28997573 0.00011
NM_000059.4(BRCA2):c.2538A>C (p.Ser846=) rs11571654 0.00009
NM_000059.4(BRCA2):c.516+18T>C rs81002834 0.00009
NM_000059.4(BRCA2):c.8215G>A (p.Val2739Ile) rs80359069 0.00009
NM_000059.4(BRCA2):c.831T>G (p.Asn277Lys) rs28897705 0.00006
NM_000059.4(BRCA2):c.8662C>T (p.Arg2888Cys) rs80359123 0.00006
NM_007294.4(BRCA1):c.2412G>C (p.Gln804His) rs55746541 0.00006
NM_000059.4(BRCA2):c.7052C>G (p.Ala2351Gly) rs80358932 0.00005
NM_000059.4(BRCA2):c.8525G>A (p.Arg2842His) rs80359105 0.00005
NM_000059.4(BRCA2):c.6143A>T (p.Asn2048Ile) rs80358853 0.00004
NM_007294.4(BRCA1):c.4357+17A>G rs80358180 0.00004
NM_007294.4(BRCA1):c.75C>T (p.Pro25=) rs80356839 0.00004
NM_000059.4(BRCA2):c.8421G>A (p.Ser2807=) rs371278843 0.00003
NM_000059.4(BRCA2):c.794-11T>C rs81002822 0.00002
NM_000059.4(BRCA2):c.4534C>T (p.Arg1512Cys) rs80358684 0.00001
NM_007294.4(BRCA1):c.2584A>G (p.Lys862Glu) rs80356927 0.00001
NM_007294.4(BRCA1):c.5096G>A (p.Arg1699Gln) rs41293459 0.00001
NM_000059.4(BRCA2):c.2803G>C (p.Asp935His) rs28897716
NM_000249.4(MLH1):c.885-21TC[2] rs267607804
NM_000314.8(PTEN):c.-511G>A rs12573787
NM_000535.7(PMS2):c.1688G>T (p.Arg563Leu) rs63750668
NM_007294.4(BRCA1):c.3952A>G (p.Ile1318Val) rs397509121
NM_024675.4(PALB2):c.2607C>T (p.Ser869=) rs45542234

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