Variants with conflicting interpretations studied for Cornelia de Lange syndrome 1

Minimum review status of the submission for Cornelia de Lange syndrome 1:		Collection method of the submission for Cornelia de Lange syndrome 1:
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
1428	182	0	37	47	0	12	90

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
Cornelia de Lange syndrome 1		pathogenic	likely pathogenic	uncertain significance	likely benign	benign
	pathogenic	0	19	5	0	0
	likely pathogenic	19	0	10	0	0
	uncertain significance	5	10	0	41	9
	likely benign	0	0	41	0	18
	benign	0	0	9	18	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
Cornelia de Lange syndrome 1	1430	180	0	37	47	0	12	90

All variants with conflicting interpretations #

Total variants: 90

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HGVS	dbSNP	gnomAD frequency
NM_133433.4(NIPBL):c.4561-9T>A	rs79924167	0.02103
NM_133433.4(NIPBL):c.1965G>T (p.Glu655Asp)	rs80358350	0.00379
NM_133433.4(NIPBL):c.535G>A (p.Ala179Thr)	rs142923613	0.00365
NM_133433.4(NIPBL):c.6109-3T>C	rs145778995	0.00363
NM_133433.4(NIPBL):c.3897T>C (p.Leu1299=)	rs80358354	0.00267
NM_133433.4(NIPBL):c.294C>T (p.Ala98=)	rs142184978	0.00134
NM_133433.4(NIPBL):c.2256A>G (p.Glu752=)	rs148075057	0.00089
NM_133433.4(NIPBL):c.2294G>A (p.Arg765Lys)	rs185678374	0.00060
NM_133433.4(NIPBL):c.1212C>T (p.Pro404=)	rs80358349	0.00048
NM_133433.4(NIPBL):c.615G>A (p.Ser205=)	rs150678035	0.00048
NM_133433.4(NIPBL):c.198C>G (p.Val66=)	rs146033170	0.00036
NM_133433.4(NIPBL):c.5011-13A>G	rs13177643	0.00036
NM_133433.4(NIPBL):c.4731A>G (p.Glu1577=)	rs140021654	0.00034
NM_133433.4(NIPBL):c.179A>G (p.Asn60Ser)	rs142703446	0.00029
NM_133433.4(NIPBL):c.2447G>A (p.Arg816His)	rs80358359	0.00028
NM_133433.4(NIPBL):c.5101T>C (p.Ser1701Pro)	rs139819353	0.00023
NM_133433.4(NIPBL):c.2603G>A (p.Arg868Gln)	rs149629686	0.00017
NM_133433.4(NIPBL):c.1833T>A (p.Ser611Arg)	rs199546324	0.00016
NM_133433.4(NIPBL):c.2903A>G (p.Asn968Ser)	rs180747605	0.00016
NM_133433.4(NIPBL):c.6478G>T (p.Asp2160Tyr)	rs147054690	0.00015
NM_133433.4(NIPBL):c.1056C>T (p.Ser352=)	rs200440893	0.00014
NM_133433.4(NIPBL):c.2448T>C (p.Arg816=)	rs139177541	0.00014
NM_133433.4(NIPBL):c.5981A>G (p.Asn1994Ser)	rs368028754	0.00011
NM_133433.4(NIPBL):c.1151A>G (p.Asn384Ser)	rs2291703	0.00009
NM_133433.4(NIPBL):c.5690A>G (p.Asn1897Ser)	rs190086412	0.00009
NM_133433.4(NIPBL):c.6589+9A>T	rs370709104	0.00009
NM_133433.4(NIPBL):c.4374T>G (p.Thr1458=)	rs749296628	0.00008
NM_133433.4(NIPBL):c.6312A>G (p.Lys2104=)	rs147865925	0.00008
NM_133433.4(NIPBL):c.5574+5G>T	rs745769829	0.00007
NM_133433.4(NIPBL):c.2219G>A (p.Gly740Asp)	rs148420552	0.00006
NM_133433.4(NIPBL):c.6438C>T (p.Thr2146=)	rs376448686	0.00006
NM_133433.4(NIPBL):c.1591A>G (p.Thr531Ala)	rs587783890	0.00005
NM_133433.4(NIPBL):c.2931A>G (p.Glu977=)	rs587783913	0.00005
NM_133433.4(NIPBL):c.1988A>C (p.Gln663Pro)	rs149892167	0.00004
NM_133433.4(NIPBL):c.2120G>T (p.Gly707Val)	rs768620796	0.00004
NM_133433.4(NIPBL):c.2768G>T (p.Gly923Val)	rs200991784	0.00003
NM_133433.4(NIPBL):c.3049A>C (p.Ile1017Leu)	rs146714879	0.00003
NM_133433.4(NIPBL):c.5762A>G (p.Asn1921Ser)	rs587783983	0.00002
NM_133433.4(NIPBL):c.8329G>T (p.Ala2777Ser)	rs200872976	0.00002
NM_133433.4(NIPBL):c.1208C>T (p.Thr403Ile)	rs746183321	0.00001
NM_133433.4(NIPBL):c.1392T>A (p.Pro464=)	rs555179389	0.00001
NM_133433.4(NIPBL):c.1434G>A (p.Glu478=)	rs750562280	0.00001
NM_133433.4(NIPBL):c.1593G>A (p.Thr531=)	rs760769176	0.00001
NM_133433.4(NIPBL):c.3102A>G (p.Lys1034=)	rs765887558	0.00001
NM_133433.4(NIPBL):c.3340G>A (p.Ala1114Thr)	rs534319970	0.00001
NM_133433.4(NIPBL):c.3423A>G (p.Ser1141=)	rs571024836	0.00001
NM_133433.4(NIPBL):c.3660G>A (p.Ala1220=)	rs143252734	0.00001
NM_133433.4(NIPBL):c.4921-4A>G	rs368263380	0.00001
NM_133433.4(NIPBL):c.5979C>T (p.Asp1993=)	rs761030463	0.00001
NM_133433.4(NIPBL):c.7068A>G (p.Lys2356=)	rs1424732133	0.00001
NM_133433.4(NIPBL):c.7411-15G>A	rs374348403	0.00001
NM_133433.4(NIPBL):c.7641C>T (p.Leu2547=)	rs587784046	0.00001
NM_133433.4(NIPBL):c.-467C>T	rs1251456909
NM_133433.4(NIPBL):c.1660C>T (p.Gln554Ter)	rs1580394197
NM_133433.4(NIPBL):c.1808del (p.Lys603fs)	rs727503767
NM_133433.4(NIPBL):c.2584A>G (p.Lys862Glu)	rs1554017428
NM_133433.4(NIPBL):c.2709A>T (p.Ser903=)	rs1256938703
NM_133433.4(NIPBL):c.2T>A (p.Met1Lys)	rs121918264
NM_133433.4(NIPBL):c.3855+5G>A	rs80358378
NM_133433.4(NIPBL):c.4321-15A>G	rs587783946
NM_133433.4(NIPBL):c.4439T>G (p.Met1480Arg)	rs587783948
NM_133433.4(NIPBL):c.5366G>A (p.Arg1789Gln)	rs80358380
NM_133433.4(NIPBL):c.5456G>A (p.Arg1819Gln)	rs80358366
NM_133433.4(NIPBL):c.5483G>A (p.Arg1828Gln)	rs587783978
NM_133433.4(NIPBL):c.5709+1G>A	rs587783979
NM_133433.4(NIPBL):c.5808+5G>A	rs2149704635
NM_133433.4(NIPBL):c.5862+1G>A	rs587783985
NM_133433.4(NIPBL):c.6068A>G (p.His2023Arg)	rs587783991
NM_133433.4(NIPBL):c.6108+7A>G	rs587783995
NM_133433.4(NIPBL):c.64+5G>A	rs587784011
NM_133433.4(NIPBL):c.6402A>G (p.Leu2134=)	rs777430704
NM_133433.4(NIPBL):c.6463G>T (p.Asp2155Tyr)
NM_133433.4(NIPBL):c.65-5A>G	rs587784012
NM_133433.4(NIPBL):c.6635T>A (p.Val2212Glu)	rs1554032789
NM_133433.4(NIPBL):c.6646T>C (p.Tyr2216His)	rs587784020
NM_133433.4(NIPBL):c.6647ATA[2] (p.Asn2218del)	rs587784022
NM_133433.4(NIPBL):c.6707A>T (p.Asn2236Ile)	rs587784023
NM_133433.4(NIPBL):c.678G>A (p.Pro226=)	rs192822119
NM_133433.4(NIPBL):c.6893G>A (p.Arg2298His)	rs587784024
NM_133433.4(NIPBL):c.7012G>C (p.Ala2338Pro)	rs587784030
NM_133433.4(NIPBL):c.7168G>A (p.Ala2390Thr)	rs587784036
NM_133433.4(NIPBL):c.7175G>A (p.Cys2392Tyr)	rs886042231
NM_133433.4(NIPBL):c.7524TTCAGA[3] (p.2508DS[3])	rs587784044
NM_133433.4(NIPBL):c.7524TTCAGA[5] (p.Ser2515_Glu2516insAspSer)
NM_133433.4(NIPBL):c.7637T>C (p.Leu2546Pro)	rs727503772
NM_133433.4(NIPBL):c.7744C>T (p.Arg2582Ter)
NM_133433.4(NIPBL):c.8300_8301del (p.Lys2767fs)	rs587784056
NM_133433.4(NIPBL):c.868+4C>T	rs751127087
NM_133433.4(NIPBL):c.894A>G (p.Gln298=)	rs587784064
NM_133433.4(NIPBL):c.9G>T (p.Gly3=)

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