Variants with conflicting interpretations studied for Hypophosphatasia

Minimum review status of the submission for Hypophosphatasia:		Collection method of the submission for Hypophosphatasia:
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
365	186	0	94	10	0	51	152

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
Hypophosphatasia		pathogenic	likely pathogenic	uncertain significance	likely benign	benign
	pathogenic	0	86	3	0	0
	likely pathogenic	68	0	48	1	0
	uncertain significance	3	46	0	9	1
	likely benign	0	1	8	0	6
	benign	0	0	1	6	0

Condition to condition summary #

Total conditions: 3

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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 confidence conflict (e.g. benign vs likely benign)	Variants with a benign or likely benign vs uncertain conflict	Variants with a clinically significant conflict (e.g. benign vs pathogenic)	Variants with any conflict
Hypophosphatasia	396	184	72	7	47	123
Adult hypophosphatasia; Childhood hypophosphatasia; Infantile hypophosphatasia	0	70	48	4	14	65
Adult hypophosphatasia; Childhood hypophosphatasia	0	1	0	0	1	1

All variants with conflicting interpretations #

Total variants: 152

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HGVS	dbSNP	gnomAD frequency
NM_000478.6(ALPL):c.1542G>T (p.Ala514=)	rs3200256	0.01113
NM_000478.6(ALPL):c.1381G>A (p.Val461Ile)	rs34810399	0.00860
NM_000478.6(ALPL):c.859T>C (p.Leu287=)	rs141742288	0.00141
NM_000478.6(ALPL):c.1482C>T (p.Leu494=)	rs142545037	0.00102
NM_000478.6(ALPL):c.818C>T (p.Thr273Met)	rs148405563	0.00101
NM_000478.6(ALPL):c.612C>T (p.Ile204=)	rs141448778	0.00067
NM_000478.6(ALPL):c.1002C>T (p.Gly334=)	rs370122334	0.00024
NM_000478.6(ALPL):c.534C>T (p.Tyr178=)	rs201250289	0.00023
NM_000478.6(ALPL):c.413G>A (p.Arg138Gln)	rs140167865	0.00017
NM_000478.6(ALPL):c.436G>A (p.Glu146Lys)	rs138587317	0.00015
NM_000478.6(ALPL):c.529G>A (p.Ala177Thr)	rs199669988	0.00011
NM_000478.6(ALPL):c.1540G>A (p.Ala514Thr)	rs367657406	0.00008
NM_000478.6(ALPL):c.1250A>G (p.Asn417Ser)	rs121918014	0.00006
NM_000478.6(ALPL):c.1446C>T (p.His482=)	rs747980975	0.00006
NM_000478.6(ALPL):c.371A>G (p.Asn124Ser)	rs11586344	0.00006
NM_000478.6(ALPL):c.575T>C (p.Met192Thr)	rs765011829	0.00006
NM_000478.6(ALPL):c.1363G>A (p.Gly455Ser)	rs149889416	0.00005
NM_000478.6(ALPL):c.1419C>T (p.Gly473=)	rs373417343	0.00005
NM_000478.6(ALPL):c.648C>T (p.Asp216=)	rs201739155	0.00005
NM_000478.6(ALPL):c.398C>G (p.Ala133Gly)	rs184095519	0.00004
NM_000478.6(ALPL):c.979T>C (p.Phe327Leu)	rs121918010	0.00004
NM_000478.6(ALPL):c.1120G>A (p.Val374Met)	rs552831415	0.00003
NM_000478.6(ALPL):c.655A>G (p.Met219Val)	rs772432010	0.00003
NM_000478.6(ALPL):c.673T>C (p.Tyr225His)	rs759125473	0.00003
NM_000478.6(ALPL):c.306C>T (p.Asn102=)	rs1015578994	0.00002
NM_000478.6(ALPL):c.44C>G (p.Thr15Ser)	rs150849772	0.00002
NM_000478.6(ALPL):c.657G>T (p.Met219Ile)	rs776117933	0.00002
NM_000478.6(ALPL):c.815G>A (p.Arg272His)	rs781272386	0.00002
NM_000478.6(ALPL):c.1022A>G (p.His341Arg)	rs1382219911	0.00001
NM_000478.6(ALPL):c.106A>C (p.Thr36Pro)	rs747167000	0.00001
NM_000478.6(ALPL):c.1078G>A (p.Gly360Arg)	rs749989499	0.00001
NM_000478.6(ALPL):c.110T>C (p.Leu37Pro)	rs143358506	0.00001
NM_000478.6(ALPL):c.1130C>T (p.Ala377Val)	rs756418235	0.00001
NM_000478.6(ALPL):c.1166C>A (p.Thr389Asn)	rs746390776	0.00001
NM_000478.6(ALPL):c.1183A>G (p.Ile395Val)	rs772682471	0.00001
NM_000478.6(ALPL):c.1271T>C (p.Val424Ala)	rs1436960562	0.00001
NM_000478.6(ALPL):c.1310C>T (p.Ala437Val)	rs1437787933	0.00001
NM_000478.6(ALPL):c.1354G>A (p.Glu452Lys)	rs966212736	0.00001
NM_000478.6(ALPL):c.1375G>A (p.Val459Met)	rs1054159992	0.00001
NM_000478.6(ALPL):c.1403C>T (p.Ala468Val)	rs766656419	0.00001
NM_000478.6(ALPL):c.1426G>A (p.Glu476Lys)	rs1057517173	0.00001
NM_000478.6(ALPL):c.1436A>G (p.Tyr479Cys)	rs1235350055	0.00001
NM_000478.6(ALPL):c.152C>T (p.Ala51Val)	rs1470389268	0.00001
NM_000478.6(ALPL):c.203C>T (p.Thr68Met)	rs1644478533	0.00001
NM_000478.6(ALPL):c.215T>C (p.Ile72Thr)	rs781264043	0.00001
NM_000478.6(ALPL):c.299C>T (p.Thr100Met)	rs1201942473	0.00001
NM_000478.6(ALPL):c.350A>G (p.Tyr117Cys)	rs1374504617	0.00001
NM_000478.6(ALPL):c.431G>A (p.Gly144Glu)	rs1291792579	0.00001
NM_000478.6(ALPL):c.484G>A (p.Gly162Ser)	rs760029254	0.00001
NM_000478.6(ALPL):c.530C>T (p.Ala177Val)	rs1114167438	0.00001
NM_000478.6(ALPL):c.542C>T (p.Ser181Leu)	rs199590449	0.00001
NM_000478.6(ALPL):c.613G>A (p.Ala205Thr)	rs751455369	0.00001
NM_000478.6(ALPL):c.643A>G (p.Ile215Val)	rs769903299	0.00001
NM_000478.6(ALPL):c.884T>C (p.Met295Thr)	rs1220125702	0.00001
NM_000478.6(ALPL):c.931G>A (p.Glu311Lys)	rs763457259	0.00001
NM_000478.6(ALPL):c.994G>T (p.Glu332Ter)	rs768976020	0.00001
NM_000478.6(ALPL):c.997+1G>T	rs1292415045	0.00001
NM_000478.6(ALPL):c.1001G>A (p.Gly334Asp)	rs121918009
NM_000478.6(ALPL):c.1010A>G (p.Asp337Gly)	rs1219494274
NM_000478.6(ALPL):c.1015G>A (p.Gly339Arg)	rs2148189619
NM_000478.6(ALPL):c.1024_1025delinsTT (p.Glu342Leu)
NM_000478.6(ALPL):c.1033G>C (p.Ala345Pro)
NM_000478.6(ALPL):c.1034C>T (p.Ala345Val)	rs1644719715
NM_000478.6(ALPL):c.1064T>C (p.Met355Thr)
NM_000478.6(ALPL):c.1077C>G (p.Ile359Met)	rs567349821
NM_000478.6(ALPL):c.1098CTC[1] (p.Ser368del)	rs1558557341
NM_000478.6(ALPL):c.1114_1115del (p.Leu372fs)	rs1553414600
NM_000478.6(ALPL):c.1132G>C (p.Asp378His)	rs1553414611
NM_000478.6(ALPL):c.1132G>T (p.Asp378Tyr)	rs1553414611
NM_000478.6(ALPL):c.113_116del (p.Lys38fs)
NM_000478.6(ALPL):c.1142A>G (p.His381Arg)	rs1558557428
NM_000478.6(ALPL):c.1144G>A (p.Val382Ile)	rs771540767
NM_000478.6(ALPL):c.1151C>G (p.Thr384Arg)	rs2148190082
NM_000478.6(ALPL):c.1162T>C (p.Tyr388His)	rs1644722881
NM_000478.6(ALPL):c.1171del (p.Arg391fs)	rs751404811
NM_000478.6(ALPL):c.1171dup (p.Arg391fs)	rs751404811
NM_000478.6(ALPL):c.1181_1182del (p.Ser394fs)	rs1344601362
NM_000478.6(ALPL):c.1189+5del	rs1208855163
NM_000478.6(ALPL):c.1195G>A (p.Ala399Thr)
NM_000478.6(ALPL):c.1207A>C (p.Ser403Arg)
NM_000478.6(ALPL):c.1213A>C (p.Thr405Pro)	rs2545347156
NM_000478.6(ALPL):c.1240C>A (p.Leu414Met)	rs2148192444
NM_000478.6(ALPL):c.1243T>G (p.Tyr415Asp)	rs2148192455
NM_000478.6(ALPL):c.1252G>A (p.Gly418Arg)
NM_000478.6(ALPL):c.1258G>A (p.Gly420Ser)	rs1644740557
NM_000478.6(ALPL):c.1259G>C (p.Gly420Ala)	rs2545347491
NM_000478.6(ALPL):c.1276G>A (p.Gly426Ser)	rs770548228
NM_000478.6(ALPL):c.1277G>A (p.Gly426Asp)	rs2545347584
NM_000478.6(ALPL):c.1283G>A (p.Arg428Gln)	rs1644741201
NM_000478.6(ALPL):c.1285G>A (p.Glu429Lys)	rs1553414868
NM_000478.6(ALPL):c.1328C>T (p.Ala443Val)	rs768053120
NM_000478.6(ALPL):c.1366G>A (p.Gly456Arg)	rs121918016
NM_000478.6(ALPL):c.1375G>T (p.Val459Leu)	rs1054159992
NM_000478.6(ALPL):c.1399A>G (p.Met467Val)
NM_000478.6(ALPL):c.1426G>T (p.Glu476Ter)	rs1057517173
NM_000478.6(ALPL):c.1427A>C (p.Glu476Ala)	rs2148195004
NM_000478.6(ALPL):c.1444C>T (p.His482Tyr)	rs780857373
NM_000478.6(ALPL):c.1447G>A (p.Val483Met)
NM_000478.6(ALPL):c.146A>T (p.Asn49Ile)	rs868522953
NM_000478.6(ALPL):c.1471G>C (p.Gly491Arg)
NM_000478.6(ALPL):c.1474del (p.Ala492fs)	rs1558558976
NM_000478.6(ALPL):c.1483G>A (p.Gly495Ser)	rs761079751
NM_000478.6(ALPL):c.1487A>G (p.His496Arg)	rs1644757200
NM_000478.6(ALPL):c.1491_1492del (p.Ala498fs)
NM_000478.6(ALPL):c.1557C>A (p.Pro519=)	rs376020180
NM_000478.6(ALPL):c.178G>C (p.Asp60His)	rs1644472852
NM_000478.6(ALPL):c.17T>C (p.Leu6Ser)
NM_000478.6(ALPL):c.182-1G>A
NM_000478.6(ALPL):c.188G>T (p.Gly63Val)	rs1490668038
NM_000478.6(ALPL):c.194C>A (p.Ser65Tyr)	rs1644478359
NM_000478.6(ALPL):c.212G>C (p.Arg71Pro)	rs121918003
NM_000478.6(ALPL):c.21_32delinsGTGT (p.Leu8fs)	rs1644366950
NM_000478.6(ALPL):c.223G>A (p.Gly75Ser)	rs1304394441
NM_000478.6(ALPL):c.244G>A (p.Gly82Arg)	rs2545292224
NM_000478.6(ALPL):c.244G>C (p.Gly82Arg)	rs2545292224
NM_000478.6(ALPL):c.247G>T (p.Glu83Ter)	rs2148152544
NM_000478.6(ALPL):c.286G>C (p.Ala96Pro)	rs2545292484
NM_000478.6(ALPL):c.297+1G>A
NM_000478.6(ALPL):c.297+5G>A	rs776187726
NM_000478.6(ALPL):c.304_312dup (p.Asn104_Ala105insAsnThrAsn)
NM_000478.6(ALPL):c.334G>A (p.Gly112Ser)	rs1384701659
NM_000478.6(ALPL):c.344C>T (p.Thr115Ile)	rs2545298833
NM_000478.6(ALPL):c.361G>A (p.Val121Met)	rs1476072388
NM_000478.6(ALPL):c.379A>G (p.Thr127Ala)	rs1570273880
NM_000478.6(ALPL):c.380C>T (p.Thr127Ile)
NM_000478.6(ALPL):c.395C>T (p.Ala132Val)	rs1558548925
NM_000478.6(ALPL):c.41T>C (p.Leu14Pro)	rs2148135377
NM_000478.6(ALPL):c.457T>C (p.Trp153Arg)	rs1644512630
NM_000478.6(ALPL):c.485G>T (p.Gly162Val)	rs121918012
NM_000478.6(ALPL):c.495CAC[1] (p.Thr167del)	rs2545303392
NM_000478.6(ALPL):c.508A>G (p.Asn170Asp)	rs2148161378
NM_000478.6(ALPL):c.50C>T (p.Ser17Phe)
NM_000478.6(ALPL):c.560A>G (p.Tyr187Cys)	rs2545303934
NM_000478.6(ALPL):c.62-1G>C
NM_000478.6(ALPL):c.644T>C (p.Ile215Thr)
NM_000478.6(ALPL):c.650delinsCTAA (p.Val217delinsAlaLys)	rs1553413155
NM_000478.6(ALPL):c.653T>C (p.Ile218Thr)
NM_000478.6(ALPL):c.675_676insCA (p.Met226fs)	rs2545317081
NM_000478.6(ALPL):c.69_74del	rs2148150789
NM_000478.6(ALPL):c.715G>T (p.Asp239Tyr)	rs1416572796
NM_000478.6(ALPL):c.738G>T (p.Arg246Ser)	rs1223142821
NM_000478.6(ALPL):c.793-30_793-11del	rs2545324149
NM_000478.6(ALPL):c.815G>T (p.Arg272Leu)	rs781272386
NM_000478.6(ALPL):c.82T>G (p.Tyr28Asp)
NM_000478.6(ALPL):c.855C>G (p.Tyr285Ter)	rs2545324707
NM_000478.6(ALPL):c.874C>A (p.Pro292Thr)	rs765458125
NM_000478.6(ALPL):c.876_882delinsT (p.Gly293_Asp294del)	rs1553414078
NM_000478.6(ALPL):c.928dup (p.Ser310fs)
NM_000478.6(ALPL):c.94C>T (p.Gln32Ter)	rs1209147330
NM_000478.6(ALPL):c.997+2T>G	rs1057517391
NM_000478.6(ALPL):c.997+3A>C	rs1553414147
NM_000478.6(ALPL):c.997+3A>G	rs1553414147

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