Variants with conflicting interpretations studied for Alpha thalassemia-X-linked intellectual disability syndrome

Minimum review status of the submission for Alpha thalassemia-X-linked intellectual disability syndrome:		Collection method of the submission for Alpha thalassemia-X-linked intellectual disability 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
2005	95	0	38	87	0	4	128

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
Alpha thalassemia-X-linked intellectual disability syndrome		pathogenic	likely pathogenic	uncertain significance	likely benign	benign
	pathogenic	0	4	1	1	1
	likely pathogenic	4	0	2	0	0
	uncertain significance	1	2	0	67	20
	likely benign	1	0	67	0	34
	benign	1	0	20	34	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
Alpha thalassemia-X-linked intellectual disability syndrome	2005	95	0	38	87	0	4	128

All variants with conflicting interpretations #

Total variants: 128

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HGVS	dbSNP	gnomAD frequency
NM_000489.6(ATRX):c.5579A>G (p.Asn1860Ser)	rs45439799	0.00640
NM_000489.6(ATRX):c.3541G>C (p.Val1181Leu)	rs61758732	0.00137
NM_000489.6(ATRX):c.1423C>G (p.His475Asp)	rs146863015	0.00050
NM_000489.6(ATRX):c.2923G>A (p.Asp975Asn)	rs200709847	0.00049
NM_000489.6(ATRX):c.4120+4A>C	rs200420513	0.00046
NM_000489.6(ATRX):c.1825C>G (p.Pro609Ala)	rs186742436	0.00035
NM_000489.6(ATRX):c.1648A>G (p.Ser550Gly)	rs201284965	0.00015
NM_000489.6(ATRX):c.2650G>A (p.Glu884Lys)	rs200343648	0.00013
NM_000489.6(ATRX):c.7256A>G (p.Asn2419Ser)	rs781853125	0.00012
NM_000489.6(ATRX):c.2806G>C (p.Val936Leu)	rs149232501	0.00010
NM_000489.6(ATRX):c.3065G>A (p.Arg1022Gln)	rs781811015	0.00009
NM_000489.6(ATRX):c.6871A>G (p.Ile2291Val)	rs374244026	0.00009
NM_000489.6(ATRX):c.7435A>G (p.Met2479Val)	rs200478641	0.00008
NM_000489.6(ATRX):c.831C>T (p.Val277=)	rs142561199	0.00008
NM_000489.6(ATRX):c.3913A>C (p.Lys1305Gln)	rs782708557	0.00007
NM_000489.6(ATRX):c.4130A>G (p.Glu1377Gly)	rs782553301	0.00007
NM_000489.6(ATRX):c.1033G>A (p.Ala345Thr)	rs149249195	0.00006
NM_000489.6(ATRX):c.1245C>T (p.Ser415=)	rs141815992	0.00006
NM_000489.6(ATRX):c.2105A>G (p.Asn702Ser)	rs782409603	0.00006
NM_000489.6(ATRX):c.2312C>T (p.Ala771Val)	rs376906761	0.00006
NM_000489.6(ATRX):c.2313G>A (p.Ala771=)	rs373458498	0.00006
NM_000489.6(ATRX):c.1169G>A (p.Arg390His)	rs367986587	0.00005
NM_000489.6(ATRX):c.118A>G (p.Met40Val)	rs149990714	0.00005
NM_000489.6(ATRX):c.1478A>G (p.His493Arg)	rs947189709	0.00005
NM_000489.6(ATRX):c.1645A>G (p.Ser549Gly)	rs148513102	0.00005
NM_000489.6(ATRX):c.2133T>G (p.Pro711=)	rs782781621	0.00005
NM_000489.6(ATRX):c.2652G>C (p.Glu884Asp)	rs782123222	0.00005
NM_000489.6(ATRX):c.2683G>C (p.Val895Leu)	rs782529714	0.00005
NM_000489.6(ATRX):c.2697G>A (p.Thr899=)	rs137974888	0.00005
NM_000489.6(ATRX):c.2701A>G (p.Ile901Val)	rs587778087	0.00005
NM_000489.6(ATRX):c.3622A>G (p.Ile1208Val)	rs782257568	0.00005
NM_000489.6(ATRX):c.3978A>G (p.Ser1326=)	rs369658928	0.00005
NM_000489.6(ATRX):c.5957-9C>G	rs375791318	0.00005
NM_000489.6(ATRX):c.1047C>G (p.Pro349=)	rs200288042	0.00004
NM_000489.6(ATRX):c.1438A>G (p.Thr480Ala)	rs587780284	0.00004
NM_000489.6(ATRX):c.2001G>A (p.Pro667=)	rs139997330	0.00004
NM_000489.6(ATRX):c.2484G>C (p.Met828Ile)	rs782705007	0.00004
NM_000489.6(ATRX):c.3091G>A (p.Gly1031Ser)	rs782781078	0.00004
NM_000489.6(ATRX):c.3555G>C (p.Lys1185Asn)	rs782696086	0.00004
NM_000489.6(ATRX):c.7439G>A (p.Arg2480Lys)	rs369871569	0.00004
NM_000489.6(ATRX):c.1257G>A (p.Ala419=)	rs185550133	0.00003
NM_000489.6(ATRX):c.2150C>T (p.Pro717Leu)	rs372617572	0.00003
NM_000489.6(ATRX):c.2225G>C (p.Ser742Thr)	rs1340328179	0.00003
NM_000489.6(ATRX):c.2696C>T (p.Thr899Met)	rs782757975	0.00003
NM_000489.6(ATRX):c.3224A>G (p.Asp1075Gly)	rs1064796745	0.00003
NM_000489.6(ATRX):c.3646A>G (p.Ile1216Val)	rs782062542	0.00003
NM_000489.6(ATRX):c.4210A>G (p.Thr1404Ala)	rs781835568	0.00003
NM_000489.6(ATRX):c.4710T>C (p.Phe1570=)	rs781829081	0.00003
NM_000489.6(ATRX):c.5073A>G (p.Gln1691=)	rs781845474	0.00003
NM_000489.6(ATRX):c.1130C>T (p.Ala377Val)	rs781955237	0.00002
NM_000489.6(ATRX):c.1346C>G (p.Pro449Arg)	rs782163488	0.00002
NM_000489.6(ATRX):c.1468G>A (p.Gly490Ser)	rs1378005125	0.00002
NM_000489.6(ATRX):c.16A>G (p.Met6Val)	rs782080475	0.00002
NM_000489.6(ATRX):c.1758A>G (p.Leu586=)	rs781987630	0.00002
NM_000489.6(ATRX):c.2118T>A (p.Ser706Arg)	rs782598442	0.00002
NM_000489.6(ATRX):c.2212C>G (p.Leu738Val)	rs782470087	0.00002
NM_000489.6(ATRX):c.3133A>G (p.Lys1045Glu)	rs1332447363	0.00002
NM_000489.6(ATRX):c.3285G>T (p.Lys1095Asn)	rs1308342676	0.00002
NM_000489.6(ATRX):c.3387G>A (p.Leu1129=)	rs3761507	0.00002
NM_000489.6(ATRX):c.3664G>A (p.Asp1222Asn)	rs782520515	0.00002
NM_000489.6(ATRX):c.631C>T (p.Arg211Cys)	rs782241890	0.00002
NM_000489.6(ATRX):c.1252C>T (p.Arg418Ter)	rs1057523785	0.00001
NM_000489.6(ATRX):c.1366G>A (p.Asp456Asn)	rs782313786	0.00001
NM_000489.6(ATRX):c.1412G>T (p.Ser471Ile)	rs1557141731	0.00001
NM_000489.6(ATRX):c.1709A>G (p.Asn570Ser)	rs782517450	0.00001
NM_000489.6(ATRX):c.1960C>G (p.Arg654Gly)	rs1557140492	0.00001
NM_000489.6(ATRX):c.2083G>C (p.Val695Leu)	rs571313578	0.00001
NM_000489.6(ATRX):c.2268A>G (p.Glu756=)	rs1243608503	0.00001
NM_000489.6(ATRX):c.2348G>C (p.Ser783Thr)	rs782530243	0.00001
NM_000489.6(ATRX):c.2472G>C (p.Glu824Asp)	rs1557139572	0.00001
NM_000489.6(ATRX):c.2648A>G (p.Gln883Arg)	rs587778086	0.00001
NM_000489.6(ATRX):c.2656G>C (p.Glu886Gln)	rs782374254	0.00001
NM_000489.6(ATRX):c.2782G>C (p.Glu928Gln)	rs797044792	0.00001
NM_000489.6(ATRX):c.2787G>C (p.Glu929Asp)	rs782283059	0.00001
NM_000489.6(ATRX):c.278A>T (p.Asp93Val)	rs1064796774	0.00001
NM_000489.6(ATRX):c.3196A>G (p.Lys1066Glu)	rs1557138007	0.00001
NM_000489.6(ATRX):c.3306G>A (p.Arg1102=)	rs782279780	0.00001
NM_000489.6(ATRX):c.3314A>G (p.Gln1105Arg)	rs1569538747	0.00001
NM_000489.6(ATRX):c.3538A>G (p.Ile1180Val)	rs782554626	0.00001
NM_000489.6(ATRX):c.3623T>C (p.Ile1208Thr)	rs374291079	0.00001
NM_000489.6(ATRX):c.3850C>T (p.Leu1284Phe)	rs782619383	0.00001
NM_000489.6(ATRX):c.4072A>G (p.Thr1358Ala)	rs781912326	0.00001
NM_000489.6(ATRX):c.4096G>A (p.Val1366Ile)	rs1280555560	0.00001
NM_000489.6(ATRX):c.4201C>T (p.Arg1401Trp)	rs1557119999	0.00001
NM_000489.6(ATRX):c.4276C>A (p.Arg1426=)	rs919106518	0.00001
NM_000489.6(ATRX):c.4862C>T (p.Thr1621Met)	rs122445106	0.00001
NM_000489.6(ATRX):c.5557C>T (p.His1853Tyr)	rs895159127	0.00001
NM_000489.6(ATRX):c.5559C>T (p.His1853=)	rs1557096973	0.00001
NM_000489.6(ATRX):c.5591G>T (p.Gly1864Val)	rs151220806	0.00001
NM_000489.6(ATRX):c.5935G>C (p.Val1979Leu)	rs782773652	0.00001
NM_000489.6(ATRX):c.6132C>T (p.Leu2044=)	rs1557079262	0.00001
NM_000489.6(ATRX):c.672G>A (p.Ala224=)	rs782223625	0.00001
NM_000489.6(ATRX):c.7379A>G (p.Tyr2460Cys)	rs782169215	0.00001
NM_000489.6(ATRX):c.847G>A (p.Val283Ile)	rs1057522580	0.00001
NM_000489.6(ATRX):c.999T>C (p.Asp333=)	rs2071429803	0.00001
NM_000489.6(ATRX):c.1212G>C (p.Lys404Asn)	rs2071413817
NM_000489.6(ATRX):c.1509A>G (p.Gln503=)	rs1039587651
NM_000489.6(ATRX):c.1526C>G (p.Thr509Ser)	rs1557141410
NM_000489.6(ATRX):c.1554G>A (p.Val518=)	rs2148619900
NM_000489.6(ATRX):c.1581C>G (p.Asp527Glu)	rs782673700
NM_000489.6(ATRX):c.1842C>T (p.Gly614=)	rs2071364653
NM_000489.6(ATRX):c.1846A>G (p.Lys616Glu)	rs2071363928
NM_000489.6(ATRX):c.1986A>G (p.Thr662=)	rs2148609958
NM_000489.6(ATRX):c.2253T>C (p.Asp751=)	rs2071332682
NM_000489.6(ATRX):c.2262T>G (p.Ile754Met)	rs1557140015
NM_000489.6(ATRX):c.2451T>C (p.Tyr817=)	rs782284572
NM_000489.6(ATRX):c.2519G>C (p.Arg840Thr)	rs191682105
NM_000489.6(ATRX):c.2592G>T (p.Gly864=)	rs782526944
NM_000489.6(ATRX):c.3064C>T (p.Arg1022Ter)	rs2071246388
NM_000489.6(ATRX):c.3090G>C (p.Lys1030Asn)	rs1557138210
NM_000489.6(ATRX):c.3137_3145del (p.Ser1046_Lys1048del)	rs781799810
NM_000489.6(ATRX):c.3440A>G (p.Lys1147Arg)	rs1461556034
NM_000489.6(ATRX):c.3456C>G (p.Gly1152=)	rs2071214967
NM_000489.6(ATRX):c.39A>G (p.Thr13=)	rs1244422748
NM_000489.6(ATRX):c.4569T>C (p.Ile1523=)	rs2148360789
NM_000489.6(ATRX):c.4770C>T (p.Cys1590=)
NM_000489.6(ATRX):c.4806A>G (p.Leu1602=)	rs2522421416
NM_000489.6(ATRX):c.4809+7G>A	rs1557107147
NM_000489.6(ATRX):c.4861A>G (p.Thr1621Ala)
NM_000489.6(ATRX):c.4865C>T (p.Ala1622Val)	rs1135401793
NM_000489.6(ATRX):c.4981C>T (p.Arg1661Cys)	rs2148338047
NM_000489.6(ATRX):c.5566+5A>C	rs782212670
NM_000489.6(ATRX):c.5787-24GTTT[4]	rs782072699
NM_000489.6(ATRX):c.5968TCT[2] (p.Ser1992del)	rs782391479
NM_000489.6(ATRX):c.6254G>A (p.Arg2085His)	rs1057517948
NM_000489.6(ATRX):c.6699+8T>C	rs2520410263
NM_000489.6(ATRX):c.711T>C (p.Asn237=)	rs782710787
NM_000489.6(ATRX):c.765A>G (p.Thr255=)	rs2520025822

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