ClinVar Miner

Variants with conflicting interpretations studied for BAP1-related tumor predisposition syndrome

Coded as:
Minimum review status of the submission for BAP1-related tumor predisposition syndrome: Collection method of the submission for BAP1-related tumor predisposition syndrome:
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
1841 171 0 18 13 0 5 35

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
BAP1-related tumor predisposition syndrome pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 4 2 0 0
likely pathogenic 4 0 3 0 0
uncertain significance 2 3 0 13 1
likely benign 0 0 13 0 14
benign 0 0 1 14 0

Condition to condition summary #

Total conditions: 1
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
BAP1-related tumor predisposition syndrome 1841 171 0 18 13 0 5 35

All variants with conflicting interpretations #

Total variants: 35
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_004656.4(BAP1):c.2057-4G>T rs149499021 0.00433
NM_004656.4(BAP1):c.1838C>T (p.Thr613Met) rs35448940 0.00377
NM_004656.4(BAP1):c.783G>A (p.Gln261=) rs35003777 0.00377
NM_004656.4(BAP1):c.1729+8T>C rs150945583 0.00364
NM_004656.4(BAP1):c.1002A>G (p.Leu334=) rs28997577 0.00310
NM_004656.4(BAP1):c.294C>T (p.Ser98=) rs140641333 0.00056
NM_004656.4(BAP1):c.1427T>C (p.Val476Ala) rs144060813 0.00044
NM_004656.4(BAP1):c.905C>T (p.Pro302Leu) rs149158790 0.00041
NM_004656.4(BAP1):c.1035G>C (p.Gly345=) rs369744075 0.00035
NM_004656.4(BAP1):c.1962A>C (p.Val654=) rs148624125 0.00031
NM_004656.4(BAP1):c.1330A>G (p.Thr444Ala) rs374746213 0.00027
NM_004656.4(BAP1):c.1735G>A (p.Gly579Arg) rs370004702 0.00013
NM_004656.4(BAP1):c.869A>G (p.Asn290Ser) rs747079481 0.00008
NM_004656.4(BAP1):c.1749G>A (p.Ser583=) rs147775249 0.00007
NM_004656.4(BAP1):c.1338C>T (p.Asn446=) rs763735807 0.00005
NM_004656.4(BAP1):c.878C>T (p.Pro293Leu) rs777664260 0.00004
NM_004656.4(BAP1):c.2175G>A (p.Lys725=) rs760537008 0.00003
NM_004656.4(BAP1):c.1251-11G>A rs981419588 0.00002
NM_004656.4(BAP1):c.177G>A (p.Arg59=) rs770446947 0.00001
NM_004656.4(BAP1):c.341G>A (p.Arg114His) rs773494626 0.00001
NM_004656.4(BAP1):c.581-4C>T rs1578225974 0.00001
NM_004656.4(BAP1):c.581-6C>T rs754576458 0.00001
NM_004656.4(BAP1):c.1202_1203del (p.Asp400_Tyr401insTer) rs886058705
NM_004656.4(BAP1):c.1554G>T (p.Arg518=) rs1705043802
NM_004656.4(BAP1):c.1869del (p.Ser623fs)
NM_004656.4(BAP1):c.1983+4G>A rs2153226279
NM_004656.4(BAP1):c.2012del (p.Tyr671fs)
NM_004656.4(BAP1):c.277A>G (p.Thr93Ala) rs375129361
NM_004656.4(BAP1):c.422A>G (p.His141Arg) rs1705201896
NM_004656.4(BAP1):c.535C>T (p.Arg179Trp) rs910211860
NM_004656.4(BAP1):c.592del (p.Glu198fs) rs1205668341
NM_004656.4(BAP1):c.659+3A>C rs878854741
NM_004656.4(BAP1):c.783+11T>C rs1705153387
NM_004656.4(BAP1):c.793_817dup (p.Thr273fs)
NM_004656.4(BAP1):c.821A>C (p.His274Pro) rs565400314

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