ClinVar Miner

Variants with conflicting interpretations studied for Schimke immuno-osseous dysplasia

Coded as:
Minimum review status of the submission for Schimke immuno-osseous dysplasia: Collection method of the submission for Schimke immuno-osseous dysplasia:
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
834 141 0 21 33 0 4 53

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
Schimke immuno-osseous dysplasia pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 10 2 0 0
likely pathogenic 10 0 4 0 0
uncertain significance 2 4 0 31 5
likely benign 0 0 31 0 11
benign 0 0 5 11 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
Schimke immuno-osseous dysplasia 834 141 0 21 33 0 4 53

All variants with conflicting interpretations #

Total variants: 53
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_014140.4(SMARCAL1):c.603G>C (p.Gly201=) rs35048226 0.00259
NM_014140.4(SMARCAL1):c.1212G>A (p.Ala404=) rs2066525 0.00241
NM_014140.4(SMARCAL1):c.1995C>T (p.Ala665=) rs151241914 0.00237
NM_014140.4(SMARCAL1):c.1271A>T (p.Asp424Val) rs2066520 0.00215
NM_014140.4(SMARCAL1):c.2528+5G>C rs145908212 0.00131
NM_014140.4(SMARCAL1):c.1196C>T (p.Thr399Met) rs139872089 0.00129
NM_014140.4(SMARCAL1):c.1851+5G>A rs2066514 0.00122
NM_014140.4(SMARCAL1):c.2528+15G>A rs200879397 0.00078
NM_014140.4(SMARCAL1):c.863-9C>G rs188833040 0.00063
NM_014140.4(SMARCAL1):c.124A>G (p.Ile42Val) rs199905841 0.00059
NM_014140.4(SMARCAL1):c.962G>A (p.Gly321Asp) rs148752234 0.00047
NM_014140.4(SMARCAL1):c.1727T>C (p.Ile576Thr) rs138819354 0.00042
NM_014140.4(SMARCAL1):c.2641A>C (p.Lys881Gln) rs190386780 0.00037
NM_014140.4(SMARCAL1):c.1785C>T (p.Ile595=) rs145825654 0.00029
NM_014140.4(SMARCAL1):c.1948G>A (p.Val650Ile) rs200734842 0.00029
NM_014140.4(SMARCAL1):c.270C>T (p.His90=) rs150591090 0.00029
NM_014140.4(SMARCAL1):c.1001G>A (p.Arg334Gln) rs138575228 0.00022
NM_014140.4(SMARCAL1):c.2114C>T (p.Thr705Ile) rs200644381 0.00019
NM_014140.4(SMARCAL1):c.1413C>T (p.Ile471=) rs149599324 0.00014
NM_014140.4(SMARCAL1):c.2542G>T (p.Glu848Ter) rs119473033 0.00013
NM_014140.4(SMARCAL1):c.2226G>A (p.Thr742=) rs2271335 0.00009
NM_014140.4(SMARCAL1):c.812-15T>C rs375588610 0.00009
NM_014140.4(SMARCAL1):c.2649C>T (p.Tyr883=) rs182217350 0.00008
NM_014140.4(SMARCAL1):c.927C>T (p.Ser309=) rs139949668 0.00006
NM_014140.4(SMARCAL1):c.735C>T (p.Gly245=) rs149510554 0.00005
NM_014140.4(SMARCAL1):c.1147+8G>A rs759562755 0.00004
NM_014140.4(SMARCAL1):c.1251G>A (p.Thr417=) rs372331472 0.00004
NM_014140.4(SMARCAL1):c.448G>T (p.Ala150Ser) rs376295895 0.00004
NM_014140.4(SMARCAL1):c.1407C>T (p.Ile469=) rs750621192 0.00003
NM_014140.4(SMARCAL1):c.1414G>A (p.Ala472Thr) rs571392819 0.00003
NM_014140.4(SMARCAL1):c.1761C>T (p.Pro587=) rs781340148 0.00003
NM_014140.4(SMARCAL1):c.888G>A (p.Thr296=) rs140707035 0.00003
NM_014140.4(SMARCAL1):c.600G>A (p.Ser200=) rs530505647 0.00002
NM_014140.4(SMARCAL1):c.1360C>T (p.Leu454=) rs753714268 0.00001
NM_014140.4(SMARCAL1):c.1374C>T (p.Asp458=) rs200566186 0.00001
NM_014140.4(SMARCAL1):c.1439C>T (p.Pro480Leu) rs758367100 0.00001
NM_014140.4(SMARCAL1):c.1756C>T (p.Arg586Trp) rs119473038 0.00001
NM_014140.4(SMARCAL1):c.1934G>A (p.Arg645His) rs1281345070 0.00001
NM_014140.4(SMARCAL1):c.1944C>T (p.Ser648=) rs752241342 0.00001
NM_014140.4(SMARCAL1):c.2290C>T (p.Arg764Trp) rs1480919035 0.00001
NM_014140.4(SMARCAL1):c.2316A>G (p.Gln772=) rs1322248626 0.00001
NM_014140.4(SMARCAL1):c.780A>G (p.Ala260=) rs1288231534 0.00001
NM_014140.4(SMARCAL1):c.1146_1147+2del rs1574450161
NM_014140.4(SMARCAL1):c.1485+8G>A rs886055617
NM_014140.4(SMARCAL1):c.1687C>T (p.Arg563Ter) rs1694125419
NM_014140.4(SMARCAL1):c.1736C>T (p.Ser579Leu) rs1694331040
NM_014140.4(SMARCAL1):c.1930C>T (p.Arg644Trp) rs1313658611
NM_014140.4(SMARCAL1):c.2295G>A (p.Glu765=) rs1301876154
NM_014140.4(SMARCAL1):c.2427+1G>A rs1559138455
NM_014140.4(SMARCAL1):c.369_370del (p.Pro124fs) rs1574443257
NM_014140.4(SMARCAL1):c.863-4G>T rs1693689203
NM_014140.4(SMARCAL1):c.960C>T (p.Ala320=) rs2066513
NM_014140.4(SMARCAL1):c.961G>A (p.Gly321Ser) rs371378288

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