Variants with conflicting interpretations studied for Pyridoxine-dependent epilepsy

Minimum review status of the submission for Pyridoxine-dependent epilepsy:		Collection method of the submission for Pyridoxine-dependent epilepsy:
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
804	131	0	49	22	0	9	78

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
Pyridoxine-dependent epilepsy		pathogenic	likely pathogenic	uncertain significance	likely benign	benign
	pathogenic	0	35	4	0	0
	likely pathogenic	35	0	7	0	0
	uncertain significance	4	7	0	21	1
	likely benign	0	0	21	0	14
	benign	0	0	1	14	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
Pyridoxine-dependent epilepsy	804	131	0	49	22	0	9	78
Pyridoxine-dependent epilepsy caused by ALDH7A1 mutant	0	1	0	1	0	0	0	1

All variants with conflicting interpretations #

Total variants: 78

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HGVS	dbSNP	gnomAD frequency
NM_001182.5(ALDH7A1):c.1009-6G>A	rs138056453	0.00463
NM_001182.5(ALDH7A1):c.1567A>G (p.Thr523Ala)	rs61757684	0.00449
NM_001182.5(ALDH7A1):c.1234A>G (p.Thr412Ala)	rs2306618	0.00338
NC_000005.10:g.126595278A>C	rs563928852	0.00294
NM_001182.5(ALDH7A1):c.373A>G (p.Ile125Val)	rs117295656	0.00178
NM_001182.5(ALDH7A1):c.1406G>A (p.Arg469His)	rs147940248	0.00118
NM_001182.4(ALDH7A1):c.-29T>C	rs556650006	0.00100
NM_001182.5(ALDH7A1):c.243A>G (p.Arg81=)	rs146438406	0.00088
NM_001182.5(ALDH7A1):c.34del (p.Ala12fs)	rs750693623	0.00054
NM_001182.5(ALDH7A1):c.774-18G>A	rs185333013	0.00043
NM_001182.5(ALDH7A1):c.494G>C (p.Gly165Ala)	rs375491094	0.00040
NM_001182.5(ALDH7A1):c.203C>A (p.Thr68Asn)	rs58528748	0.00032
NM_001182.5(ALDH7A1):c.858G>A (p.Val286=)	rs150623275	0.00031
NM_001182.5(ALDH7A1):c.39A>G (p.Ala13=)	rs201566142	0.00025
NM_001182.5(ALDH7A1):c.1279G>C (p.Glu427Gln)	rs121912707	0.00023
NM_001182.5(ALDH7A1):c.1276A>G (p.Thr426Ala)	rs150305320	0.00019
NM_001182.5(ALDH7A1):c.193-20C>T	rs199762757	0.00018
NM_001182.5(ALDH7A1):c.528T>C (p.His176=)	rs757135576	0.00018
NM_001182.5(ALDH7A1):c.423G>C (p.Val141=)	rs199653162	0.00016
NM_001182.5(ALDH7A1):c.393+15T>C	rs183254966	0.00015
NM_001182.5(ALDH7A1):c.1016A>G (p.His339Arg)	rs199767457	0.00010
NM_001182.5(ALDH7A1):c.1305C>G (p.Val435=)	rs142975776	0.00010
NM_001182.5(ALDH7A1):c.1287T>C (p.Phe429=)	rs375030056	0.00009
NM_001182.5(ALDH7A1):c.774-19C>T	rs373058643	0.00009
NM_001182.5(ALDH7A1):c.313-15G>A	rs201720741	0.00008
NM_001182.5(ALDH7A1):c.200C>T (p.Thr67Met)	rs543181020	0.00007
NM_001182.5(ALDH7A1):c.834G>A (p.Val278=)	rs201948406	0.00005
NM_001182.5(ALDH7A1):c.913+8T>C	rs766528289	0.00005
NM_001182.5(ALDH7A1):c.1017T>C (p.His339=)	rs200394848	0.00004
NM_001182.5(ALDH7A1):c.1068G>A (p.Gln356=)	rs376004978	0.00004
NM_001182.5(ALDH7A1):c.1405C>T (p.Arg469Cys)	rs752523070	0.00004
NM_001182.5(ALDH7A1):c.364C>T (p.Arg122Trp)	rs370624118	0.00004
NM_001182.5(ALDH7A1):c.720C>T (p.Asp240=)	rs757704473	0.00004
NM_001182.5(ALDH7A1):c.1411_1412insG (p.Leu471fs)	rs772766995	0.00003
NM_001182.5(ALDH7A1):c.1547A>G (p.Tyr516Cys)	rs200102503	0.00003
NM_001182.5(ALDH7A1):c.201G>T (p.Thr67=)	rs747643987	0.00003
NM_001182.5(ALDH7A1):c.394-15G>A	rs766287925	0.00003
NM_001182.5(ALDH7A1):c.664A>G (p.Thr222Ala)	rs777829351	0.00003
NM_001182.5(ALDH7A1):c.965C>T (p.Ala322Val)	rs777483675	0.00003
NM_001182.5(ALDH7A1):c.1004G>A (p.Arg335Gln)	rs754449549	0.00002
NM_001182.5(ALDH7A1):c.332G>A (p.Gly111Glu)	rs994001880	0.00002
NM_001182.5(ALDH7A1):c.607T>G (p.Trp203Gly)	rs555896752	0.00002
NM_001182.5(ALDH7A1):c.1008+11C>T	rs367574304	0.00001
NM_001182.5(ALDH7A1):c.1061A>G (p.Tyr354Cys)	rs1471249688	0.00001
NM_001182.5(ALDH7A1):c.1200+1G>T	rs1217642695	0.00001
NM_001182.5(ALDH7A1):c.1292C>T (p.Pro431Leu)	rs151107837	0.00001
NM_001182.5(ALDH7A1):c.1344T>A (p.Asn448Lys)	rs2480252837	0.00001
NM_001182.5(ALDH7A1):c.1375A>T (p.Ile459Phe)	rs186558364	0.00001
NM_001182.5(ALDH7A1):c.1415+15A>G	rs370757950	0.00001
NM_001182.5(ALDH7A1):c.1489+5G>A	rs368820286	0.00001
NM_001182.5(ALDH7A1):c.1536C>T (p.Ala512=)	rs1015790945	0.00001
NM_001182.5(ALDH7A1):c.1556G>A (p.Arg519Lys)	rs561343926	0.00001
NM_001182.5(ALDH7A1):c.1565+1G>T	rs1064793830	0.00001
NM_001182.5(ALDH7A1):c.222C>T (p.Asn74=)	rs1007871645	0.00001
NM_001182.5(ALDH7A1):c.246+1G>A	rs764588746	0.00001
NM_001182.5(ALDH7A1):c.312+1G>A	rs199497486	0.00001
NM_001182.5(ALDH7A1):c.530C>A (p.Ala177Glu)	rs764417585	0.00001
NM_001182.5(ALDH7A1):c.575C>T (p.Thr192Met)	rs376917645	0.00001
NM_001182.5(ALDH7A1):c.921A>G (p.Glu307=)	rs1750312383	0.00001
NM_001182.5(ALDH7A1):c.950C>T (p.Ser317Leu)	rs148052962	0.00001
NM_001182.5(ALDH7A1):c.1171G>T (p.Glu391Ter)	rs1750104210
NM_001182.5(ALDH7A1):c.1301_1302del (p.Tyr434fs)	rs753671880
NM_001182.5(ALDH7A1):c.141_142insA (p.Arg48fs)	rs1296037862
NM_001182.5(ALDH7A1):c.1439T>C (p.Ile480Thr)	rs886059849
NM_001182.5(ALDH7A1):c.1531G>A (p.Asp511Asn)	rs2480242765
NM_001182.5(ALDH7A1):c.1553G>C (p.Arg518Thr)	rs749231711
NM_001182.5(ALDH7A1):c.1597del (p.Ala533fs)	rs387906574
NM_001182.5(ALDH7A1):c.187G>T (p.Gly63Ter)	rs760636660
NM_001182.5(ALDH7A1):c.285_286insG (p.Arg96fs)	rs758414053
NM_001182.5(ALDH7A1):c.313-10C>A	rs567441242
NM_001182.5(ALDH7A1):c.494G>T (p.Gly165Val)	rs375491094
NM_001182.5(ALDH7A1):c.605G>A (p.Gly202Asp)	rs899342601
NM_001182.5(ALDH7A1):c.651-18T>A	rs2112792324
NM_001182.5(ALDH7A1):c.848G>A (p.Gly283Asp)	rs1181991285
NM_001182.5(ALDH7A1):c.859C>T (p.Gln287Ter)	rs1204010423
NM_001182.5(ALDH7A1):c.901_902del (p.Asn301fs)	rs1064794240
NM_001182.5(ALDH7A1):c.902A>T (p.Asn301Ile)	rs121912711
NM_001182.5(ALDH7A1):c.979G>A (p.Gly327Ser)	rs1554099008

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