Variants with conflicting interpretations studied for Peroxisome biogenesis disorder 1A (Zellweger)

Minimum review status of the submission for Peroxisome biogenesis disorder 1A (Zellweger):		Collection method of the submission for Peroxisome biogenesis disorder 1A (Zellweger):
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
102	62	0	63	39	0	7	106

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
Peroxisome biogenesis disorder 1A (Zellweger)		pathogenic	likely pathogenic	uncertain significance	likely benign	benign
	pathogenic	0	13	0	0	0
	likely pathogenic	51	0	3	1	0
	uncertain significance	4	7	0	36	12
	likely benign	0	0	3	0	5
	benign	0	0	0	1	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
Zellweger spectrum disorders	0	59	0	63	39	0	7	106
Peroxisome biogenesis disorder 1A (Zellweger)	243	14	0	7	3	0	3	13

All variants with conflicting interpretations #

Total variants: 106

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HGVS	dbSNP	gnomAD frequency
NM_000466.3(PEX1):c.1671-7T>C	rs74519968	0.01312
NM_000466.3(PEX1):c.3720C>T (p.His1240=)	rs34825053	0.00582
NM_000318.3(PEX2):c.748T>C (p.Trp250Arg)	rs142645936	0.00573
NM_000466.3(PEX1):c.330C>G (p.Pro110=)	rs71560821	0.00220
NM_000466.3(PEX1):c.1579A>G (p.Thr527Ala)	rs144942544	0.00217
NM_000466.3(PEX1):c.2442C>T (p.Phe814=)	rs145430946	0.00216
NM_000466.3(PEX1):c.3810T>A (p.Ser1270Arg)	rs139054881	0.00188
NM_000466.3(PEX1):c.637C>T (p.Leu213Phe)	rs141798874	0.00171
NM_000466.3(PEX1):c.1011G>A (p.Lys337=)	rs142018583	0.00155
NM_000466.3(PEX1):c.130-9T>C	rs377337949	0.00145
NM_000466.3(PEX1):c.2926+8T>C	rs369877998	0.00084
NM_000466.3(PEX1):c.3216T>C (p.Ser1072=)	rs140963147	0.00069
NM_000466.3(PEX1):c.3373A>T (p.Met1125Leu)	rs142994610	0.00065
NM_000466.3(PEX1):c.2792C>A (p.Ala931Asp)	rs144825021	0.00055
NM_000466.3(PEX1):c.2718+3A>G	rs370536529	0.00040
NM_000466.3(PEX1):c.3031G>A (p.Val1011Met)	rs141650598	0.00036
NM_000466.3(PEX1):c.1360-4G>T	rs199716270	0.00034
NM_000466.3(PEX1):c.939T>C (p.His313=)	rs199647157	0.00034
NM_000466.3(PEX1):c.1360-7C>T	rs371890000	0.00029
NM_000466.3(PEX1):c.2528G>A (p.Gly843Asp)	rs61750420	0.00025
NM_000466.3(PEX1):c.1725G>A (p.Leu575=)	rs150667796	0.00022
NM_000466.3(PEX1):c.627G>A (p.Met209Ile)	rs200752969	0.00016
NM_000466.3(PEX1):c.3250A>G (p.Met1084Val)	rs781277635	0.00014
NM_000466.3(PEX1):c.1587+5T>C	rs199526105	0.00011
NM_000466.3(PEX1):c.3637-14T>C	rs745612436	0.00009
NM_000466.3(PEX1):c.1042A>G (p.Thr348Ala)	rs371309198	0.00006
NM_000466.3(PEX1):c.2842C>T (p.Arg948Trp)	rs374167385	0.00006
NM_000466.3(PEX1):c.1441G>A (p.Val481Ile)	rs139919229	0.00005
NM_000466.3(PEX1):c.147G>A (p.Val49=)	rs202230667	0.00005
NM_000466.3(PEX1):c.2383C>T (p.Arg795Ter)	rs61750418	0.00005
NM_000466.3(PEX1):c.2584-10T>C	rs375129444	0.00005
NM_000466.3(PEX1):c.2927-12T>A	rs375062546	0.00005
NM_000466.3(PEX1):c.2846G>A (p.Arg949Gln)	rs61750425	0.00004
NM_000466.3(PEX1):c.3165A>G (p.Gln1055=)	rs776231556	0.00003
NM_000466.3(PEX1):c.2730del (p.Leu910fs)	rs61750423	0.00002
NM_000466.3(PEX1):c.2T>C (p.Met1Thr)	rs766020928	0.00002
NM_000466.3(PEX1):c.3166T>C (p.Leu1056=)	rs1009877821	0.00002
NM_000466.3(PEX1):c.782_783del (p.Gln261fs)	rs749067142	0.00002
NM_000287.4(PEX6):c.2435G>A (p.Arg812Gln)	rs61753229	0.00001
NM_000466.3(PEX1):c.1671-13A>G	rs757960956	0.00001
NM_000466.3(PEX1):c.1777G>A (p.Gly593Arg)	rs61750407	0.00001
NM_000466.3(PEX1):c.1897C>T (p.Arg633Ter)	rs61750409	0.00001
NM_000466.3(PEX1):c.1991T>C (p.Leu664Pro)	rs121434455	0.00001
NM_000466.3(PEX1):c.1A>T (p.Met1Leu)	rs1057517501	0.00001
NM_000466.3(PEX1):c.2230C>T (p.Gln744Ter)	rs398123409	0.00001
NM_000466.3(PEX1):c.2845C>T (p.Arg949Trp)	rs866184460	0.00001
NM_000466.3(PEX1):c.2859dup (p.Thr954fs)	rs1057517472	0.00001
NM_000466.3(PEX1):c.2926+2T>C	rs267608180	0.00001
NM_000466.3(PEX1):c.2927-8T>C	rs778618662	0.00001
NM_000466.3(PEX1):c.3038G>A (p.Arg1013His)	rs1484321655	0.00001
NM_000466.3(PEX1):c.3195G>A (p.Ser1065=)	rs768417678	0.00001
NM_000466.3(PEX1):c.3543A>G (p.Ser1181=)	rs374673391	0.00001
NM_000466.3(PEX1):c.3642C>T (p.Asp1214=)	rs777384403	0.00001
NM_000466.3(PEX1):c.5G>A (p.Trp2Ter)	rs762679408	0.00001
NM_000466.3(PEX1):c.96G>A (p.Pro32=)	rs1445565547	0.00001
NM_000466.3(PEX1):c.1076del (p.Lys359fs)	rs1057517465
NM_000466.3(PEX1):c.1108del (p.Ile370fs)	rs61750406
NM_000466.3(PEX1):c.129+10C>T	rs886062508
NM_000466.3(PEX1):c.130-2A>T	rs1585260993
NM_000466.3(PEX1):c.1380A>C (p.Glu460Asp)	rs565049190
NM_000466.3(PEX1):c.1501_1502del (p.Leu501fs)	rs786204743
NM_000466.3(PEX1):c.1522dup (p.Glu508fs)	rs1057517463
NM_000466.3(PEX1):c.1528G>T (p.Glu510Ter)	rs754983126
NM_000466.3(PEX1):c.1670+1G>A	rs1057517490
NM_000466.3(PEX1):c.1670+1G>T	rs1057517490
NM_000466.3(PEX1):c.1716_1717del (p.His572fs)	rs786204606
NM_000466.3(PEX1):c.1804-12A>G	rs143041528
NM_000466.3(PEX1):c.1838_1839dup (p.Lys614fs)	rs1554372561
NM_000466.3(PEX1):c.1842del (p.Glu615fs)	rs267608176
NM_000466.3(PEX1):c.1886_1887del (p.Asp628_Cys629insTer)	rs1398892633
NM_000466.3(PEX1):c.1901-14T>C	rs1792111444
NM_000466.3(PEX1):c.1908del (p.Arg636fs)	rs1057517478
NM_000466.3(PEX1):c.1927del (p.Thr643fs)	rs1554372180
NM_000466.3(PEX1):c.1927dup (p.Thr643fs)	rs1554372180
NM_000466.3(PEX1):c.1A>C (p.Met1Leu)	rs1057517501
NM_000466.3(PEX1):c.2034_2035del (p.His678fs)	rs61750412
NM_000466.3(PEX1):c.2137C>T (p.Gln713Ter)	rs1057517468
NM_000466.3(PEX1):c.2162_2166del (p.Leu721fs)	rs1057517499
NM_000466.3(PEX1):c.2391_2392del (p.Arg798fs)	rs61750414
NM_000466.3(PEX1):c.2633TGT[1] (p.Leu879del)	rs886043984
NM_000466.3(PEX1):c.2686C>T (p.Arg896Ter)	rs1057517485
NM_000466.3(PEX1):c.2760del (p.Ala921fs)	rs1256376226
NM_000466.3(PEX1):c.2798dup (p.Pro934fs)	rs1057517484
NM_000466.3(PEX1):c.2852dup (p.His951fs)	rs767877383
NM_000466.3(PEX1):c.2873_2875delinsT (p.Asp958fs)	rs2116094537
NM_000466.3(PEX1):c.2875C>T (p.Arg959Ter)	rs1057517481
NM_000466.3(PEX1):c.2916del (p.Gly973fs)	rs61750426
NM_000466.3(PEX1):c.2922del (p.Leu974fs)	rs762324548
NM_000466.3(PEX1):c.2992C>T (p.Arg998Ter)	rs61750428
NM_000466.3(PEX1):c.2T>G (p.Met1Arg)	rs766020928
NM_000466.3(PEX1):c.3037C>T (p.Arg1013Cys)	rs1791439311
NM_000466.3(PEX1):c.3077T>C (p.Leu1026Pro)	rs954814470
NM_000466.3(PEX1):c.3152_3156del (p.Leu1051fs)	rs2116077430
NM_000466.3(PEX1):c.3455_3456del (p.Ser1152fs)	rs759183382
NM_000466.3(PEX1):c.357+1G>T	rs866144313
NM_000466.3(PEX1):c.3574C>T (p.Gln1192Ter)	rs1057517467
NM_000466.3(PEX1):c.3579del (p.Asp1194fs)	rs1554366802
NM_000466.3(PEX1):c.3627C>T (p.Ser1209=)	rs886062501
NM_000466.3(PEX1):c.3693_3696del (p.Gln1231fs)	rs769836601
NM_000466.3(PEX1):c.3G>A (p.Met1Ile)	rs786204704
NM_000466.3(PEX1):c.403C>T (p.Arg135Ter)	rs201415996
NM_000466.3(PEX1):c.468A>G (p.Gln156=)	rs149729088
NM_000466.3(PEX1):c.473-1G>A	rs1554375661
NM_000466.3(PEX1):c.569C>A (p.Ser190Ter)	rs1554375599
NM_000466.3(PEX1):c.643_647del (p.Thr215fs)	rs786204544
NM_000466.3(PEX1):c.911_912del (p.Ser304fs)	rs786204638

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