Variants with conflicting interpretations studied for Severe early-childhood-onset retinal dystrophy

Minimum review status of the submission for Severe early-childhood-onset retinal dystrophy:		Collection method of the submission for Severe early-childhood-onset retinal dystrophy:
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
451	59	1	93	1	1	11	103

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
Severe early-childhood-onset retinal dystrophy		pathogenic	likely pathogenic	uncertain significance	likely benign	benign	other
	pathogenic	1	78	4	0	0	1
	likely pathogenic	85	0	5	0	0	1
	uncertain significance	6	7	0	0	1	1
	likely benign	0	0	0	0	1	0
	benign	0	0	1	1	0	0
	other	1	1	1	0	0	0

Condition to condition summary #

Total conditions: 2

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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
Severe early-childhood-onset retinal dystrophy	487	48	1	72	1	1	6	78
Stargardt disease	0	27	0	51	0	1	7	57

All variants with conflicting interpretations #

Total variants: 103

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HGVS	dbSNP	gnomAD frequency
NM_000350.3(ABCA4):c.5603A>T (p.Asn1868Ile)	rs1801466	0.04034
NM_000350.3(ABCA4):c.2828G>A (p.Arg943Gln)	rs1801581	0.02951
NM_000350.3(ABCA4):c.3602T>G (p.Leu1201Arg)	rs61750126	0.02687
NM_000350.3(ABCA4):c.6320G>A (p.Arg2107His)	rs62642564	0.00654
NM_000350.3(ABCA4):c.4253+43G>A	rs61754045	0.00486
NM_000350.3(ABCA4):c.2588G>C (p.Gly863Ala)	rs76157638	0.00445
NM_000350.3(ABCA4):c.5908C>T (p.Leu1970Phe)	rs28938473	0.00362
NM_000350.3(ABCA4):c.6148G>C (p.Val2050Leu)	rs41292677	0.00304
NM_000350.3(ABCA4):c.455G>A (p.Arg152Gln)	rs62646862	0.00287
NM_000350.3(ABCA4):c.5882G>A (p.Gly1961Glu)	rs1800553	0.00269
NM_000350.3(ABCA4):c.4771G>A (p.Gly1591Arg)	rs113106943	0.00232
NM_000350.3(ABCA4):c.2971G>C (p.Gly991Arg)	rs61749455	0.00194
NM_000350.3(ABCA4):c.3113C>T (p.Ala1038Val)	rs61751374	0.00164
NM_000350.3(ABCA4):c.5693G>A (p.Arg1898His)	rs1800552	0.00147
NM_000350.3(ABCA4):c.2791G>A (p.Val931Met)	rs58331765	0.00136
NM_000350.3(ABCA4):c.1411G>A (p.Glu471Lys)	rs1800548	0.00089
NM_000350.3(ABCA4):c.5077G>A (p.Val1693Ile)	rs61750563	0.00082
NM_000350.3(ABCA4):c.1532G>A (p.Arg511His)	rs140482171	0.00048
NM_000350.3(ABCA4):c.6089G>A (p.Arg2030Gln)	rs61750641	0.00048
NM_000350.3(ABCA4):c.6316C>T (p.Arg2106Cys)	rs61750648	0.00034
NM_000350.3(ABCA4):c.5714+5G>A	rs61751407	0.00032
NM_000350.3(ABCA4):c.5461-10T>C	rs1800728	0.00029
NM_000350.3(ABCA4):c.6119G>A (p.Arg2040Gln)	rs148460146	0.00024
NM_000350.3(ABCA4):c.4139C>T (p.Pro1380Leu)	rs61750130	0.00023
NM_000350.3(ABCA4):c.3386G>T (p.Arg1129Leu)	rs1801269	0.00022
NM_000350.3(ABCA4):c.3322C>T (p.Arg1108Cys)	rs61750120	0.00019
NM_000350.3(ABCA4):c.6079C>T (p.Leu2027Phe)	rs61751408	0.00018
NM_000350.3(ABCA4):c.1622T>C (p.Leu541Pro)	rs61751392	0.00017
NM_000350.3(ABCA4):c.4577C>T (p.Thr1526Met)	rs61750152	0.00016
NM_000350.3(ABCA4):c.5338C>G (p.Pro1780Ala)	rs121909207	0.00014
NM_000350.3(ABCA4):c.5196+1137G>A	rs778234759	0.00012
NM_000350.3(ABCA4):c.4457C>T (p.Pro1486Leu)	rs61750145	0.00009
NM_000350.3(ABCA4):c.71G>A (p.Arg24His)	rs62645958	0.00009
NM_000350.3(ABCA4):c.634C>T (p.Arg212Cys)	rs61750200	0.00008
NM_000350.3(ABCA4):c.4610C>T (p.Thr1537Met)	rs62642575	0.00007
NM_000350.3(ABCA4):c.2453G>A (p.Gly818Glu)	rs61750202	0.00006
NM_000350.3(ABCA4):c.768G>T (p.Val256=)	rs62645944	0.00006
NM_000350.3(ABCA4):c.1294G>A (p.Glu432Lys)	rs201117452	0.00005
NM_000350.3(ABCA4):c.1715G>A (p.Arg572Gln)	rs61748559	0.00005
NM_000350.3(ABCA4):c.4469G>A (p.Cys1490Tyr)	rs61751402	0.00005
NM_000350.3(ABCA4):c.4519G>A (p.Gly1507Arg)	rs568792949	0.00005
NM_000350.3(ABCA4):c.4594G>A (p.Asp1532Asn)	rs62642574	0.00005
NM_000350.3(ABCA4):c.6449G>A (p.Cys2150Tyr)	rs61751384	0.00005
NM_000350.3(ABCA4):c.2300T>A (p.Val767Asp)	rs61751395	0.00004
NM_000350.3(ABCA4):c.3056C>T (p.Thr1019Met)	rs201855602	0.00003
NM_000350.3(ABCA4):c.4195G>A (p.Glu1399Lys)	rs62642573	0.00003
NM_000350.3(ABCA4):c.4328G>A (p.Arg1443His)	rs61750142	0.00003
NM_000350.3(ABCA4):c.4539+2001G>A	rs1457937638	0.00003
NM_000350.3(ABCA4):c.5381C>A (p.Ala1794Asp)	rs61751406	0.00003
NM_000350.3(ABCA4):c.5413A>G (p.Asn1805Asp)	rs61753029	0.00003
NM_000350.3(ABCA4):c.5761G>A (p.Val1921Met)	rs61753032	0.00003
NM_000350.3(ABCA4):c.5819T>C (p.Leu1940Pro)	rs61753033	0.00003
NM_000350.3(ABCA4):c.6721C>G (p.Leu2241Val)	rs61748521	0.00003
NM_000350.3(ABCA4):c.179C>T (p.Ala60Val)	rs55732384	0.00002
NM_000350.3(ABCA4):c.3364G>A (p.Glu1122Lys)	rs61751399	0.00002
NM_000350.3(ABCA4):c.4919G>A (p.Arg1640Gln)	rs61751403	0.00002
NM_000350.3(ABCA4):c.1335C>G (p.Ser445Arg)	rs61748552	0.00001
NM_000350.3(ABCA4):c.1822T>A (p.Phe608Ile)	rs61752398	0.00001
NM_000350.3(ABCA4):c.1903C>T (p.Gln635Ter)	rs61749414	0.00001
NM_000350.3(ABCA4):c.1957C>T (p.Arg653Cys)	rs61749420	0.00001
NM_000350.3(ABCA4):c.1A>G (p.Met1Val)	rs201738997	0.00001
NM_000350.3(ABCA4):c.2401G>A (p.Ala801Thr)	rs374410829	0.00001
NM_000350.3(ABCA4):c.3064G>A (p.Glu1022Lys)	rs61749459	0.00001
NM_000350.3(ABCA4):c.3352C>T (p.His1118Tyr)	rs369440533	0.00001
NM_000350.3(ABCA4):c.3482G>A (p.Arg1161His)	rs768278935	0.00001
NM_000350.3(ABCA4):c.4234C>T (p.Gln1412Ter)	rs61750137	0.00001
NM_000350.3(ABCA4):c.4253+4C>T	rs61754044	0.00001
NM_000350.3(ABCA4):c.4352+1G>A	rs200967229	0.00001
NM_000350.3(ABCA4):c.4462T>C (p.Cys1488Arg)	rs61750146	0.00001
NM_000350.3(ABCA4):c.4463G>T (p.Cys1488Phe)	rs61750147	0.00001
NM_000350.3(ABCA4):c.454C>T (p.Arg152Ter)	rs62646861	0.00001
NM_000350.3(ABCA4):c.4748T>C (p.Leu1583Pro)	rs61750153	0.00001
NM_000350.3(ABCA4):c.4793C>A (p.Ala1598Asp)	rs61750155	0.00001
NM_000350.3(ABCA4):c.4926C>G (p.Ser1642Arg)	rs61753017	0.00001
NM_000350.3(ABCA4):c.4978C>T (p.Pro1660Ser)	rs1211325812	0.00001
NM_000350.3(ABCA4):c.5018+2T>C	rs61750562	0.00001
NM_000350.3(ABCA4):c.5113C>T (p.Arg1705Trp)	rs771038310	0.00001
NM_000350.3(ABCA4):c.5316G>A (p.Trp1772Ter)	rs61750571	0.00001
NM_000350.3(ABCA4):c.5318C>T (p.Ala1773Val)	rs760549861	0.00001
NM_000350.3(ABCA4):c.6088C>T (p.Arg2030Ter)	rs61751383	0.00001
NM_000350.3(ABCA4):c.6118C>T (p.Arg2040Ter)	rs61753038	0.00001
NM_000350.3(ABCA4):c.6306C>A (p.Asp2102Glu)	rs568627877	0.00001
NM_000350.3(ABCA4):c.6445C>T (p.Arg2149Ter)	rs61750654	0.00001
NM_000350.3(ABCA4):c.6658C>T (p.Gln2220Ter)	rs61753046	0.00001
NM_000350.3(ABCA4):c.885del (p.Leu296fs)	rs764759172	0.00001
NM_000350.2(ABCA4):c.[1622T>C;3113C>T]
NM_000350.3(ABCA4):c.1357-2A>G	rs886044726
NM_000350.3(ABCA4):c.1621_1622del (p.Leu541fs)	rs1553192715
NM_000350.3(ABCA4):c.1846G>A (p.Glu616Lys)	rs1557787473
NM_000350.3(ABCA4):c.194G>A (p.Gly65Glu)	rs62654395
NM_000350.3(ABCA4):c.2041C>T (p.Arg681Ter)	rs61749423
NM_000350.3(ABCA4):c.286A>G (p.Asn96Asp)	rs61748529
NM_000350.3(ABCA4):c.2875A>G (p.Thr959Ala)	rs368846708
NM_000350.3(ABCA4):c.3210_3211dup (p.Ser1071fs)	rs387906385
NM_000350.3(ABCA4):c.3323G>T (p.Arg1108Leu)	rs61750121
NM_000350.3(ABCA4):c.4537dup (p.Gln1513fs)	rs281865377
NM_000350.3(ABCA4):c.4854G>C (p.Trp1618Cys)	rs61752439
NM_000350.3(ABCA4):c.4979C>T (p.Pro1660Leu)	rs886044746
NM_000350.3(ABCA4):c.5196+2T>C	rs61751405
NM_000350.3(ABCA4):c.5512C>G (p.His1838Asp)	rs62642562
NM_000350.3(ABCA4):c.5584+6T>C	rs61750633
NM_000350.3(ABCA4):c.6238_6239del (p.Ser2080fs)	rs281865382
NM_000350.3(ABCA4):c.6308C>A (p.Pro2103His)	rs2100994049

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