Variants with conflicting interpretations studied for Alkaptonuria

Minimum review status of the submission for Alkaptonuria:		Collection method of the submission for Alkaptonuria:
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
453	52	0	67	13	0	20	93

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
Alkaptonuria		pathogenic	likely pathogenic	uncertain significance	likely benign	benign
	pathogenic	0	59	15	3	2
	likely pathogenic	59	0	6	0	1
	uncertain significance	15	6	0	13	0
	likely benign	3	0	13	0	8
	benign	2	1	0	8	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
Alkaptonuria	453	52	0	67	13	0	20	93

All variants with conflicting interpretations #

Total variants: 93

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HGVS	dbSNP	gnomAD frequency
NM_000187.4(HGD):c.1221G>A (p.Ala407=)	rs146206905	0.01639
NM_000187.4(HGD):c.142G>T (p.Ala48Ser)	rs138846036	0.01021
NM_000187.4(HGD):c.1179T>C (p.Asp393=)	rs146482816	0.00926
NM_000187.4(HGD):c.260A>C (p.Glu87Ala)	rs35702995	0.00392
NM_000187.4(HGD):c.711C>A (p.Arg237=)	rs147204182	0.00276
NM_000187.4(HGD):c.129G>A (p.Gln43=)	rs142789485	0.00165
NM_000187.4(HGD):c.919C>T (p.Arg307Cys)	rs143556739	0.00124
NM_000187.4(HGD):c.221A>T (p.Glu74Val)	rs141965690	0.00027
NM_000187.4(HGD):c.8A>C (p.Glu3Ala)	rs200412910	0.00022
NM_000187.4(HGD):c.307C>A (p.Pro103Thr)	rs559502955	0.00017
NM_000187.4(HGD):c.1097G>A (p.Ser366Asn)	rs759101002	0.00015
NM_000187.4(HGD):c.1176C>T (p.Ala392=)	rs368805723	0.00013
NM_000187.4(HGD):c.1112A>G (p.His371Arg)	rs120074172	0.00012
NM_000187.4(HGD):c.141G>A (p.Ser47=)	rs541268108	0.00011
NM_000187.4(HGD):c.1206A>G (p.Ser402=)	rs140500816	0.00009
NM_000187.4(HGD):c.125A>C (p.Glu42Ala)	rs373921680	0.00007
NM_000187.4(HGD):c.550-14G>C	rs769000073	0.00006
NM_000187.4(HGD):c.808G>A (p.Gly270Arg)	rs120074174	0.00006
NM_000187.4(HGD):c.158G>A (p.Arg53Gln)	rs200808744	0.00005
NM_000187.4(HGD):c.177-5T>C	rs768308376	0.00004
NM_000187.4(HGD):c.502G>A (p.Glu168Lys)	rs375283568	0.00004
NM_000187.4(HGD):c.899T>G (p.Val300Gly)	rs120074170	0.00004
NM_000187.4(HGD):c.367G>A (p.Gly123Arg)	rs564979861	0.00003
NM_000187.4(HGD):c.709C>T (p.Arg237Cys)	rs1171237852	0.00003
NM_000187.4(HGD):c.765T>C (p.Ala255=)	rs747764475	0.00003
NM_000187.4(HGD):c.990G>T (p.Arg330Ser)	rs120074171	0.00003
NM_000187.4(HGD):c.1120G>C (p.Asp374His)	rs981454067	0.00002
NM_000187.4(HGD):c.1336T>C (p.Ter446Arg)	rs143370662	0.00002
NM_000187.4(HGD):c.342+1G>T	rs397515518	0.00002
NM_000187.4(HGD):c.1076C>T (p.Pro359Leu)	rs764037565	0.00001
NM_000187.4(HGD):c.11T>A (p.Leu4Ter)	rs786204422	0.00001
NM_000187.4(HGD):c.1266C>T (p.Asn422=)	rs1417213536	0.00001
NM_000187.4(HGD):c.140C>T (p.Ser47Leu)	rs369517993	0.00001
NM_000187.4(HGD):c.15+1G>A	rs552207335	0.00001
NM_000187.4(HGD):c.157C>T (p.Arg53Trp)	rs759435977	0.00001
NM_000187.4(HGD):c.343G>C (p.Gly115Arg)	rs755734596	0.00001
NM_000187.4(HGD):c.347T>C (p.Leu116Pro)	rs569846003	0.00001
NM_000187.4(HGD):c.365C>T (p.Ala122Val)	rs544956641	0.00001
NM_000187.4(HGD):c.37G>A (p.Glu13Lys)	rs1458752246	0.00001
NM_000187.4(HGD):c.469+2T>C	rs745333667	0.00001
NM_000187.4(HGD):c.473C>T (p.Pro158Leu)	rs375396766	0.00001
NM_000187.4(HGD):c.504G>C (p.Glu168Asp)	rs780173554	0.00001
NM_000187.4(HGD):c.536T>G (p.Ile179Ser)	rs1031569954	0.00001
NM_000187.4(HGD):c.587C>T (p.Thr196Ile)	rs781491692	0.00001
NM_000187.4(HGD):c.673C>T (p.Arg225Cys)	rs756789146	0.00001
NM_000187.4(HGD):c.674G>A (p.Arg225His)	rs562853291	0.00001
NM_000187.4(HGD):c.752G>A (p.Gly251Asp)	rs781011621	0.00001
NM_000187.4(HGD):c.821C>T (p.Pro274Leu)	rs1397264922	0.00001
NM_000187.4(HGD):c.1039C>T (p.Arg347Ter)	rs975005146
NM_000187.4(HGD):c.1040G>C (p.Arg347Pro)	rs1414633272
NM_000187.4(HGD):c.105C>A (p.Cys35Ter)	rs2472801382
NM_000187.4(HGD):c.1081G>A (p.Gly361Arg)	rs765219004
NM_000187.4(HGD):c.1114G>A (p.Gly372Arg)	rs1940645842
NM_000187.4(HGD):c.1188+1G>T	rs760206323
NM_000187.4(HGD):c.11T>C (p.Leu4Ser)	rs786204422
NM_000187.4(HGD):c.1201G>C (p.Glu401Gln)	rs767159114
NM_000187.4(HGD):c.127C>G (p.Gln43Glu)	rs1243059404
NM_000187.4(HGD):c.1290_1300del (p.Lys431fs)	rs1553715351
NM_000187.4(HGD):c.131T>C (p.Leu44Pro)	rs1708095030
NM_000187.4(HGD):c.179G>A (p.Trp60Ter)	rs1057516467
NM_000187.4(HGD):c.189G>T (p.Arg63Ser)	rs1390061303
NM_000187.4(HGD):c.283-5del	rs777429123
NM_000187.4(HGD):c.289T>G (p.Trp97Gly)	rs2472725122
NM_000187.4(HGD):c.291G>A (p.Trp97Ter)	rs766714128
NM_000187.4(HGD):c.31_32delinsATT (p.Gly11fs)	rs1057516362
NM_000187.4(HGD):c.334T>G (p.Phe112Val)	rs2472724557
NM_000187.4(HGD):c.342+1G>A	rs397515518
NM_000187.4(HGD):c.342+3A>C	rs1182670238
NM_000187.4(HGD):c.346del (p.Leu116fs)	rs1057516911
NM_000187.4(HGD):c.368G>A (p.Gly123Glu)	rs374473331
NM_000187.4(HGD):c.376_377del (p.Lys126fs)	rs1057516976
NM_000187.4(HGD):c.3G>C (p.Met1Ile)	rs1057516355
NM_000187.4(HGD):c.447T>A (p.Asn149Lys)	rs2107513499
NM_000187.4(HGD):c.455G>C (p.Gly152Ala)	rs1553717936
NM_000187.4(HGD):c.474G>A (p.Pro158=)	rs2293734
NM_000187.4(HGD):c.474G>T (p.Pro158=)	rs2293734
NM_000187.4(HGD):c.482G>A (p.Gly161Glu)	rs1941187762
NM_000187.4(HGD):c.513G>T (p.Lys171Asn)	rs2472701853
NM_000187.4(HGD):c.532G>T (p.Glu178Ter)	rs1941184654
NM_000187.4(HGD):c.549G>T (p.Gln183His)	rs759615683
NM_000187.4(HGD):c.557T>A (p.Met186Lys)	rs1941163113
NM_000187.4(HGD):c.559C>G (p.Arg187Gly)	rs756255206
NM_000187.4(HGD):c.566G>T (p.Ser189Ile)	rs2107510544
NM_000187.4(HGD):c.583G>T (p.Glu195Ter)	rs1184695718
NM_000187.4(HGD):c.647T>C (p.Ile216Thr)	rs767201131
NM_000187.4(HGD):c.649+2T>C	rs1057516307
NM_000187.4(HGD):c.652del	rs786204662
NM_000187.4(HGD):c.665C>A (p.Ala222Asp)	rs1576294110
NM_000187.4(HGD):c.674G>C (p.Arg225Pro)	rs562853291
NM_000187.4(HGD):c.753C>T (p.Gly251=)	rs1357020990
NM_000187.4(HGD):c.87+1G>A	rs2472804506
NM_000187.4(HGD):c.880-4A>G	rs781667761
NM_000187.4(HGD):c.970dup (p.Val324fs)	rs34214309

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