Variants with conflicting interpretations studied for Schimke immuno-osseous dysplasia

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: Report conflict between different conditions
Show significances as they were submitted (without aggregation into standard terms)

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
959	167	0	41	53	0	5	93

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	30	3	0	0
	likely pathogenic	30	0	5	0	0
	uncertain significance	3	5	0	51	5
	likely benign	0	0	51	0	11
	benign	0	0	5	11	0

Condition to condition summary #

Total conditions: 1

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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	959	167	0	41	53	0	5	93

All variants with conflicting interpretations #

Total variants: 93

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HGVS	dbSNP	gnomAD frequency
NM_014140.4(SMARCAL1):c.1212G>A (p.Ala404=)	rs2066525	0.00241
NM_014140.4(SMARCAL1):c.603G>C (p.Gly201=)	rs35048226	0.00234
NM_014140.4(SMARCAL1):c.1995C>T (p.Ala665=)	rs151241914	0.00217
NM_014140.4(SMARCAL1):c.1271A>T (p.Asp424Val)	rs2066520	0.00205
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	0.00115
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	0.00055
NM_014140.4(SMARCAL1):c.962G>A (p.Gly321Asp)	rs148752234	0.00045
NM_014140.4(SMARCAL1):c.1727T>C (p.Ile576Thr)	rs138819354	0.00042
NM_014140.4(SMARCAL1):c.2641A>C (p.Lys881Gln)	rs190386780	0.00035
NM_014140.4(SMARCAL1):c.2226G>A (p.Thr742=)	rs2271335	0.00031
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.1785C>T (p.Ile595=)	rs145825654	0.00027
NM_014140.4(SMARCAL1):c.1001G>A (p.Arg334Gln)	rs138575228	0.00019
NM_014140.4(SMARCAL1):c.2114C>T (p.Thr705Ile)	rs200644381	0.00015
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.1414G>A (p.Ala472Thr)	rs571392819	0.00009
NM_014140.4(SMARCAL1):c.2070+2dup	rs762716070	0.00009
NM_014140.4(SMARCAL1):c.2142-15C>A	rs371522763	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.836T>C (p.Phe279Ser)	rs775057827	0.00006
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.1069T>A (p.Phe357Ile)	rs369180164	0.00003
NM_014140.4(SMARCAL1):c.1407C>T (p.Ile469=)	rs750621192	0.00003
NM_014140.4(SMARCAL1):c.1761C>T (p.Pro587=)	rs781340148	0.00003
NM_014140.4(SMARCAL1):c.2534T>A (p.Leu845Gln)	rs372298863	0.00003
NM_014140.4(SMARCAL1):c.353C>G (p.Ala118Gly)	rs776290743	0.00003
NM_014140.4(SMARCAL1):c.888G>A (p.Thr296=)	rs140707035	0.00003
NM_014140.4(SMARCAL1):c.926G>A (p.Ser309Asn)	rs545116067	0.00003
NM_014140.4(SMARCAL1):c.1374C>T (p.Asp458=)	rs200566186	0.00002
NM_014140.4(SMARCAL1):c.2459G>A (p.Arg820His)	rs200666300	0.00002
NM_014140.4(SMARCAL1):c.600G>A (p.Ser200=)	rs530505647	0.00002
NM_014140.4(SMARCAL1):c.1158G>A (p.Val386=)	rs769875821	0.00001
NM_014140.4(SMARCAL1):c.1191del (p.Thr399fs)	rs956223874	0.00001
NM_014140.4(SMARCAL1):c.1360C>T (p.Leu454=)	rs753714268	0.00001
NM_014140.4(SMARCAL1):c.1439C>T (p.Pro480Leu)	rs758367100	0.00001
NM_014140.4(SMARCAL1):c.1645-19T>A	rs757704897	0.00001
NM_014140.4(SMARCAL1):c.1756C>T (p.Arg586Trp)	rs119473038	0.00001
NM_014140.4(SMARCAL1):c.1931G>A (p.Arg644Gln)	rs140515579	0.00001
NM_014140.4(SMARCAL1):c.1933C>T (p.Arg645Cys)	rs119473037	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.2295G>A (p.Glu765=)	rs1301876154	0.00001
NM_014140.4(SMARCAL1):c.2316A>G (p.Gln772=)	rs1322248626	0.00001
NM_014140.4(SMARCAL1):c.2520C>T (p.Asp840=)	rs1325007410	0.00001
NM_014140.4(SMARCAL1):c.2529-7C>G	rs758029017	0.00001
NM_014140.4(SMARCAL1):c.2535G>C (p.Leu845=)	rs777273652	0.00001
NM_014140.4(SMARCAL1):c.768G>A (p.Ala256=)	rs1436190761	0.00001
NM_014140.4(SMARCAL1):c.780A>G (p.Ala260=)	rs1288231534	0.00001
NM_014140.4(SMARCAL1):c.1051C>T (p.Gln351Ter)	rs2469621143
NM_014140.4(SMARCAL1):c.1097_1098del (p.Asp366fs)	rs2469625357
NM_014140.4(SMARCAL1):c.1146_1147+2del	rs1574450161
NM_014140.4(SMARCAL1):c.126dup (p.Ala43fs)	rs962523270
NM_014140.4(SMARCAL1):c.1334+1G>A	rs1384402545
NM_014140.4(SMARCAL1):c.1458A>C (p.Pro486=)	rs2106033735
NM_014140.4(SMARCAL1):c.1467G>T (p.Val489=)	rs145525014
NM_014140.4(SMARCAL1):c.1614G>A (p.Gln538=)	rs1320735965
NM_014140.4(SMARCAL1):c.1687C>T (p.Arg563Ter)	rs1694125419
NM_014140.4(SMARCAL1):c.1711-9G>A	rs927457751
NM_014140.4(SMARCAL1):c.1736C>T (p.Ser579Leu)	rs1694331040
NM_014140.4(SMARCAL1):c.1881del (p.Ser628fs)	rs990873729
NM_014140.4(SMARCAL1):c.1930C>T (p.Arg644Trp)	rs1313658611
NM_014140.4(SMARCAL1):c.1934_1935del (p.Arg645fs)	rs1694436631
NM_014140.4(SMARCAL1):c.1940A>C (p.Lys647Thr)	rs2106055226
NM_014140.4(SMARCAL1):c.2181G>A (p.Lys727=)	rs1694866311
NM_014140.4(SMARCAL1):c.2238G>A (p.Glu746=)	rs1191687480
NM_014140.4(SMARCAL1):c.2277C>T (p.Thr759=)	rs2106086332
NM_014140.4(SMARCAL1):c.2427+1G>A	rs1559138455
NM_014140.4(SMARCAL1):c.340C>T (p.Arg114Cys)	rs202031614
NM_014140.4(SMARCAL1):c.369_370del (p.Pro124fs)	rs1574443257
NM_014140.4(SMARCAL1):c.427_430del (p.Leu143fs)	rs1693559368
NM_014140.4(SMARCAL1):c.609del (p.Asn203fs)	rs2106015063
NM_014140.4(SMARCAL1):c.622del (p.His208fs)	rs751582760
NM_014140.4(SMARCAL1):c.641dup (p.Thr215fs)	rs2106015104
NM_014140.4(SMARCAL1):c.669G>A (p.Gln223=)	rs1350600578
NM_014140.4(SMARCAL1):c.709C>T (p.Gln237Ter)
NM_014140.4(SMARCAL1):c.777T>C (p.Ile259=)	rs1359695954
NM_014140.4(SMARCAL1):c.863-17TTC[2]	rs762653086
NM_014140.4(SMARCAL1):c.863-4G>T	rs1693689203
NM_014140.4(SMARCAL1):c.886del (p.Thr296fs)	rs2469620696
NM_014140.4(SMARCAL1):c.960C>T (p.Ala320=)	rs2066513
NM_014140.4(SMARCAL1):c.961G>A (p.Gly321Ser)	rs371378288

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