Variants with conflicting interpretations studied for X-linked Alport syndrome

Minimum review status of the submission for X-linked Alport syndrome:		Collection method of the submission for X-linked Alport syndrome:
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
1121	120	0	56	8	0	22	81

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
X-linked Alport syndrome		pathogenic	likely pathogenic	uncertain significance	likely benign	benign
	pathogenic	0	52	6	1	1
	likely pathogenic	52	0	19	0	0
	uncertain significance	6	19	0	5	4
	likely benign	1	0	5	0	4
	benign	1	0	4	4	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
X-linked Alport syndrome	1121	120	0	56	8	0	22	81

All variants with conflicting interpretations #

Total variants: 81

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HGVS	dbSNP	gnomAD frequency
NM_033380.3(COL4A5):c.1289C>A (p.Ala430Asp)	rs142883891	0.00420
NM_033380.3(COL4A5):c.2858G>T (p.Gly953Val)	rs78972735	0.00119
NM_033380.3(COL4A5):c.2215C>G (p.Pro739Ala)	rs104886164	0.00034
NM_033380.3(COL4A5):c.2692A>G (p.Met898Val)	rs104886192	0.00020
NM_033380.3(COL4A5):c.488T>C (p.Met163Thr)	rs142503631	0.00012
NM_033380.3(COL4A5):c.3403A>G (p.Ile1135Val)	rs747614562	0.00007
NM_033380.3(COL4A5):c.1871G>A (p.Gly624Asp)	rs104886142	0.00006
NM_033380.3(COL4A5):c.443C>T (p.Pro148Leu)	rs773404950	0.00004
NM_033380.3(COL4A5):c.2998G>A (p.Gly1000Arg)	rs2067110688	0.00003
NM_033380.3(COL4A5):c.5048G>A (p.Arg1683Gln)	rs104886308	0.00002
NM_033380.3(COL4A5):c.2362C>T (p.Arg788Cys)	rs762935451	0.00001
NM_033380.3(COL4A5):c.3508G>A (p.Gly1170Ser)	rs104886237	0.00001
NM_033380.3(COL4A5):c.4891C>T (p.Arg1631Cys)	rs865842167	0.00001
NM_033380.3(COL4A5):c.779A>G (p.Gln260Arg)	rs372889859	0.00001
NM_033380.3(COL4A5):c.1001G>A (p.Gly334Asp)	rs104886093
NM_033380.3(COL4A5):c.1032+17del	rs761615270
NM_033380.3(COL4A5):c.1033-6A>G	rs869025330
NM_033380.3(COL4A5):c.1091C>T (p.Pro364Leu)
NM_033380.3(COL4A5):c.1094G>A (p.Gly365Glu)	rs104886096
NM_033380.3(COL4A5):c.1117C>T (p.Arg373Ter)	rs104886094
NM_033380.3(COL4A5):c.1120G>A (p.Gly374Arg)	rs2066342176
NM_033380.3(COL4A5):c.1225G>A (p.Gly409Ser)	rs2066425550
NM_033380.3(COL4A5):c.1525G>C (p.Gly509Arg)	rs754223700
NM_033380.3(COL4A5):c.1588-10C>G	rs1603290097
NM_033380.3(COL4A5):c.1690G>C (p.Gly564Arg)	rs281874674
NM_033380.3(COL4A5):c.1690G>T (p.Gly564Cys)	rs281874674
NM_033380.3(COL4A5):c.1780G>A (p.Gly594Ser)	rs104886131
NM_033380.3(COL4A5):c.1808G>A (p.Gly603Asp)	rs104886133
NM_033380.3(COL4A5):c.1967G>A (p.Gly656Asp)	rs2066625376
NM_033380.3(COL4A5):c.2023G>A (p.Gly675Ser)	rs104886157
NM_033380.3(COL4A5):c.2165G>A (p.Gly722Glu)	rs104886163
NM_033380.3(COL4A5):c.2288G>A (p.Gly763Glu)	rs281874689
NM_033380.3(COL4A5):c.2323G>A (p.Gly775Ser)
NM_033380.3(COL4A5):c.2446C>T (p.Pro816Ser)	rs2524375503
NM_033380.3(COL4A5):c.2465G>T (p.Gly822Val)	rs1291655627
NM_033380.3(COL4A5):c.2466ACCACCAGG[1] (p.823PPG[1])	rs104886356
NM_033380.3(COL4A5):c.2473G>A (p.Gly825Arg)	rs281874692
NM_033380.3(COL4A5):c.2605G>A (p.Gly869Arg)	rs104886189
NM_033380.3(COL4A5):c.2633G>C (p.Gly878Ala)
NM_033380.3(COL4A5):c.2777G>T (p.Gly926Val)	rs2147865541
NM_033380.3(COL4A5):c.2999G>T (p.Gly1000Val)	rs281874709
NM_033380.3(COL4A5):c.3016+1G>A	rs104886377
NM_033380.3(COL4A5):c.3088G>A (p.Gly1030Ser)	rs104886210
NM_033380.3(COL4A5):c.3152G>A (p.Gly1051Glu)	rs1603298993
NM_033380.3(COL4A5):c.3197G>A (p.Gly1066Asp)	rs104886221
NM_033380.3(COL4A5):c.3293G>A (p.Gly1098Asp)	rs1603306716
NM_033380.3(COL4A5):c.3346G>A (p.Gly1116Arg)	rs2147935344
NM_033380.3(COL4A5):c.3410G>A (p.Gly1137Asp)	rs1131691795
NM_033380.3(COL4A5):c.3427G>A (p.Gly1143Ser)	rs104886228
NM_033380.3(COL4A5):c.3454+1G>C
NM_033380.3(COL4A5):c.358G>A (p.Gly120Ser)	rs2524196968
NM_033380.3(COL4A5):c.3659G>A (p.Gly1220Asp)	rs104886251
NM_033380.3(COL4A5):c.3686G>A (p.Gly1229Asp)	rs104886253
NM_033380.3(COL4A5):c.3853G>A (p.Gly1285Ser)	rs764755602
NM_033380.3(COL4A5):c.4016-1G>A	rs797045035
NM_033380.3(COL4A5):c.4283G>A (p.Arg1428His)	rs2068539626
NM_033380.3(COL4A5):c.4316-20T>A	rs2068567564
NM_033380.3(COL4A5):c.4445G>A (p.Cys1482Tyr)	rs1569508382
NM_033380.3(COL4A5):c.446del (p.Pro149fs)	rs104886054
NM_033380.3(COL4A5):c.4543T>C (p.Cys1515Arg)
NM_033380.3(COL4A5):c.4631G>A (p.Trp1544Ter)	rs104886293
NM_033380.3(COL4A5):c.4706G>A (p.Arg1569Gln)	rs281874743
NM_033380.3(COL4A5):c.476G>A (p.Gly159Asp)	rs2147759208
NM_033380.3(COL4A5):c.4783G>T (p.Gly1595Ter)	rs2524652341
NM_033380.3(COL4A5):c.4808A>G (p.Tyr1603Cys)	rs104886298
NM_033380.3(COL4A5):c.4912T>C (p.Cys1638Arg)	rs281874750
NM_033380.3(COL4A5):c.4931G>A (p.Cys1644Tyr)	rs104886302
NM_033380.3(COL4A5):c.4962G>A (p.Trp1654Ter)	rs2068718016
NM_033380.3(COL4A5):c.4964T>G (p.Leu1655Arg)	rs104886303
NM_033380.3(COL4A5):c.4994+1G>A	rs2524654509
NM_033380.3(COL4A5):c.548G>A (p.Gly183Asp)	rs104886059
NM_033380.3(COL4A5):c.556G>A (p.Gly186Ser)	rs2066140289
NM_033380.3(COL4A5):c.574G>A (p.Gly192Arg)	rs104886060
NM_033380.3(COL4A5):c.637G>C (p.Gly213Arg)	rs267606310
NM_033380.3(COL4A5):c.689G>T (p.Gly230Val)	rs281874763
NM_033380.3(COL4A5):c.866G>A (p.Gly289Asp)	rs104886450
NM_033380.3(COL4A5):c.884G>A (p.Gly295Asp)	rs104886079
NM_033380.3(COL4A5):c.919G>A (p.Gly307Ser)	rs2147777425
NM_033380.3(COL4A5):c.920G>A (p.Gly307Asp)	rs104886082
NM_033380.3(COL4A5):c.938G>T (p.Gly313Val)	rs2147781020
NM_033380.3(COL4A5):c.983G>A (p.Gly328Asp)	rs2066274585

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