Variants with conflicting interpretations studied for Cystinuria

Minimum review status of the submission for Cystinuria:		Collection method of the submission for Cystinuria:
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
567	83	0	39	26	0	27	85

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
Cystinuria		pathogenic	likely pathogenic	uncertain significance	likely benign	benign
	pathogenic	0	37	13	0	1
	likely pathogenic	37	0	16	4	0
	uncertain significance	13	16	0	20	6
	likely benign	0	4	20	0	2
	benign	1	0	6	2	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
Cystinuria	567	83	0	39	26	0	27	85

All variants with conflicting interpretations #

Total variants: 85

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HGVS	dbSNP	gnomAD frequency
NM_000341.4(SLC3A1):c.892-6C>G	rs114640930	0.00594
NM_000341.4(SLC3A1):c.300C>T (p.Leu100=)	rs115030299	0.00351
NM_000341.4(SLC3A1):c.1035G>A (p.Glu345=)	rs78795495	0.00338
NM_014270.5(SLC7A9):c.978-17G>A	rs45628833	0.00315
NM_000341.4(SLC3A1):c.566C>T (p.Thr189Met)	rs140317484	0.00287
NM_000341.4(SLC3A1):c.797T>C (p.Phe266Ser)	rs141587158	0.00273
NM_000341.4(SLC3A1):c.231T>A (p.Ser77=)	rs146630359	0.00250
NM_014270.5(SLC7A9):c.544G>A (p.Ala182Thr)	rs79389353	0.00239
NM_000341.4(SLC3A1):c.1398C>T (p.Asn466=)	rs140821819	0.00211
NM_000341.4(SLC3A1):c.1400T>C (p.Met467Thr)	rs121912691	0.00175
NM_014270.5(SLC7A9):c.1403C>T (p.Pro468Leu)	rs80283711	0.00089
NM_000341.4(SLC3A1):c.788G>C (p.Ser263Thr)	rs139310305	0.00076
NM_000341.4(SLC3A1):c.1126G>A (p.Gly376Ser)	rs143068960	0.00073
NM_000341.4(SLC3A1):c.1381T>C (p.Tyr461His)	rs144162964	0.00044
NM_014270.5(SLC7A9):c.-26G>T	rs375495587	0.00042
NM_000341.4(SLC3A1):c.1473C>T (p.Ala491=)	rs144065614	0.00028
NM_000341.4(SLC3A1):c.66C>T (p.Asn22=)	rs149507807	0.00026
NM_000341.4(SLC3A1):c.592del (p.Ala198fs)	rs778000327	0.00025
NM_014270.5(SLC7A9):c.829G>A (p.Val277Met)	rs147344717	0.00024
NM_014270.5(SLC7A9):c.368C>T (p.Thr123Met)	rs79987078	0.00023
NM_014270.5(SLC7A9):c.313G>A (p.Gly105Arg)	rs121908480	0.00018
NM_000341.4(SLC3A1):c.1889G>A (p.Gly630Asp)	rs150557210	0.00017
NM_014270.5(SLC7A9):c.782C>T (p.Pro261Leu)	rs121908486	0.00014
NM_000341.4(SLC3A1):c.1136+2T>C	rs766198611	0.00012
NM_000341.4(SLC3A1):c.417C>T (p.Asn139=)	rs150870922	0.00012
NM_014270.5(SLC7A9):c.695A>G (p.Tyr232Cys)	rs121908487	0.00012
NM_000341.4(SLC3A1):c.1973G>A (p.Arg658His)	rs370262167	0.00011
NM_014270.5(SLC7A9):c.419T>C (p.Phe140Ser)	rs752881588	0.00010
NM_000341.4(SLC3A1):c.1717T>C (p.Leu573=)	rs148703534	0.00009
NM_000341.4(SLC3A1):c.1799G>A (p.Gly600Glu)	rs141944551	0.00009
NM_000341.4(SLC3A1):c.647C>T (p.Thr216Met)	rs369641941	0.00009
NM_000341.4(SLC3A1):c.1137-3T>C	rs555017366	0.00008
NM_000341.4(SLC3A1):c.1084C>T (p.Arg362Cys)	rs375399468	0.00006
NM_000341.4(SLC3A1):c.1354C>T (p.Arg452Trp)	rs201502095	0.00006
NM_014270.5(SLC7A9):c.671C>T (p.Ala224Val)	rs140873167	0.00006
NM_000341.4(SLC3A1):c.1093C>T (p.Arg365Trp)	rs765828196	0.00005
NM_000341.4(SLC3A1):c.1826A>G (p.Asn609Ser)	rs200592320	0.00005
NM_014270.5(SLC7A9):c.604+2T>C	rs763110287	0.00005
NM_000341.4(SLC3A1):c.1125C>T (p.Pro375=)	rs760943092	0.00004
NM_000341.4(SLC3A1):c.1179C>T (p.Thr393=)	rs778276427	0.00004
NM_000341.4(SLC3A1):c.1796T>C (p.Phe599Ser)	rs146963107	0.00004
NM_000341.4(SLC3A1):c.201G>T (p.Gly67=)	rs771021431	0.00004
NM_014270.5(SLC7A9):c.511C>T (p.Arg171Trp)	rs758242098	0.00004
NM_014270.5(SLC7A9):c.997C>T (p.Arg333Trp)	rs121908484	0.00004
NM_000341.4(SLC3A1):c.1269C>T (p.Ser423=)	rs557669708	0.00003
NM_000341.4(SLC3A1):c.266T>C (p.Leu89Pro)	rs1453871309	0.00003
NM_000341.4(SLC3A1):c.1011G>A (p.Pro337=)	rs772810111	0.00002
NM_000341.4(SLC3A1):c.1085G>A (p.Arg362His)	rs121912697	0.00002
NM_000341.4(SLC3A1):c.1367G>A (p.Arg456His)	rs373852467	0.00002
NM_000341.4(SLC3A1):c.1136+10G>A	rs755742518	0.00001
NM_000341.4(SLC3A1):c.1810C>T (p.Leu604=)	rs770801300	0.00001
NM_000341.4(SLC3A1):c.1843C>A (p.Pro615Thr)	rs121912696	0.00001
NM_000341.4(SLC3A1):c.418G>A (p.Gly140Arg)	rs768848958	0.00001
NM_000341.4(SLC3A1):c.452A>G (p.Tyr151Cys)	rs778354350	0.00001
NM_014270.5(SLC7A9):c.583G>A (p.Gly195Arg)	rs121908482	0.00001
NM_014270.5(SLC7A9):c.605-3C>A	rs749913021	0.00001
NM_000341.4(SLC3A1):c.1094G>A (p.Arg365Gln)	rs567478582
NM_000341.4(SLC3A1):c.1094G>T (p.Arg365Leu)	rs567478582
NM_000341.4(SLC3A1):c.1188C>G (p.Tyr396Ter)	rs374750983
NM_000341.4(SLC3A1):c.1200A>G (p.Pro400=)	rs886056069
NM_000341.4(SLC3A1):c.1364C>T (p.Ser455Leu)
NM_000341.4(SLC3A1):c.1366C>T (p.Arg456Cys)
NM_000341.4(SLC3A1):c.1373G>T (p.Gly458Val)
NM_000341.4(SLC3A1):c.1400T>A (p.Met467Lys)	rs121912691
NM_000341.4(SLC3A1):c.1603_1604del (p.Thr535fs)	rs767801148
NM_000341.4(SLC3A1):c.1617+1dup	rs2104385579
NM_000341.4(SLC3A1):c.1640C>T (p.Ser547Leu)	rs368796166
NM_000341.4(SLC3A1):c.1749_1750del (p.Glu585fs)	rs1672820246
NM_000341.4(SLC3A1):c.1750del (p.Arg584fs)	rs775827496
NM_000341.4(SLC3A1):c.1854G>A (p.Met618Ile)	rs698761
NM_000341.4(SLC3A1):c.1945G>A (p.Glu649Lys)	rs1484579709
NM_000341.4(SLC3A1):c.1955C>G (p.Thr652Arg)	rs121912695
NM_000341.4(SLC3A1):c.1993A>T (p.Arg665Ter)
NM_000341.4(SLC3A1):c.2033T>C (p.Leu678Pro)	rs121912693
NM_000341.4(SLC3A1):c.242G>T (p.Arg81Leu)	rs201617723
NM_000341.4(SLC3A1):c.283G>A (p.Ala95Thr)
NM_000341.4(SLC3A1):c.430+1G>A
NM_000341.4(SLC3A1):c.679C>T (p.Arg227Trp)
NM_000341.4(SLC3A1):c.891+4A>G	rs2465902056
NM_014270.5(SLC7A9):c.120G>A (p.Val40=)	rs140179068
NM_014270.5(SLC7A9):c.1397C>A (p.Ser466Ter)	rs1967855547
NM_014270.5(SLC7A9):c.1399+4_1399+7del	rs747593886
NM_014270.5(SLC7A9):c.775G>A (p.Gly259Arg)	rs121908483
NM_014270.5(SLC7A9):c.878T>C (p.Phe293Ser)	rs1968696030
NM_014270.5(SLC7A9):c.992C>T (p.Ala331Val)	rs768466784

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