Variants with conflicting interpretations studied for Juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome

Minimum review status of the submission for Juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome:		Collection method of the submission for Juvenile polyposis/hereditary hemorrhagic telangiectasia 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
750	47	0	92	20	0	2	104

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
Juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome		pathogenic	likely pathogenic	uncertain significance	likely benign	benign
	pathogenic	0	4	0	0	0
	likely pathogenic	4	0	2	0	0
	uncertain significance	0	2	0	19	11
	likely benign	0	0	19	0	88
	benign	0	0	11	88	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
Juvenile polyposis/hereditary hemorrhagic telangiectasia syndrome	750	47	0	92	20	0	2	104

All variants with conflicting interpretations #

Total variants: 104

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HGVS	dbSNP	gnomAD frequency
NM_005359.6(SMAD4):c.1086T>C (p.Phe362=)	rs1801250	0.00228
NM_005359.6(SMAD4):c.1140-10T>C	rs186332162	0.00205
NM_005359.6(SMAD4):c.565C>T (p.Arg189Cys)	rs140743238	0.00104
NM_005359.6(SMAD4):c.1573A>G (p.Ile525Val)	rs149755320	0.00068
NM_005359.6(SMAD4):c.1392C>T (p.Ala464=)	rs140487104	0.00033
NM_005359.6(SMAD4):c.582A>G (p.Thr194=)	rs145805120	0.00016
NM_005359.6(SMAD4):c.521C>A (p.Thr174Asn)	rs138800446	0.00014
NM_005359.6(SMAD4):c.21G>A (p.Thr7=)	rs142292491	0.00010
NM_005359.6(SMAD4):c.424+5G>A	rs200772603	0.00010
NM_005359.6(SMAD4):c.852A>G (p.Gln284=)	rs144378484	0.00008
NM_005359.6(SMAD4):c.1647A>G (p.Gln549=)	rs113545983	0.00007
NM_005359.6(SMAD4):c.1218G>A (p.Ala406=)	rs145097078	0.00004
NM_005359.6(SMAD4):c.1608A>G (p.Leu536=)	rs753128184	0.00004
NM_005359.6(SMAD4):c.1653A>G (p.Leu551=)	rs199526820	0.00004
NM_005359.6(SMAD4):c.228A>G (p.Arg76=)	rs587780556	0.00004
NM_005359.6(SMAD4):c.1215C>T (p.His405=)	rs751732234	0.00003
NM_005359.6(SMAD4):c.1236C>T (p.Tyr412=)	rs121912577	0.00003
NM_005359.6(SMAD4):c.1644A>G (p.Pro548=)	rs756795016	0.00003
NM_005359.6(SMAD4):c.411A>G (p.Val137=)	rs201296880	0.00003
NM_005359.6(SMAD4):c.84A>G (p.Gln28=)	rs778465458	0.00003
NM_005359.6(SMAD4):c.1140-11T>A	rs1224777335	0.00002
NM_005359.6(SMAD4):c.132A>G (p.Val44=)	rs965942065	0.00002
NM_005359.6(SMAD4):c.1461T>A (p.Ala487=)	rs769607309	0.00002
NM_005359.6(SMAD4):c.1611C>T (p.Asp537=)	rs369598262	0.00002
NM_005359.6(SMAD4):c.1632G>A (p.Pro544=)	rs549489716	0.00002
NM_005359.6(SMAD4):c.294C>T (p.Leu98=)	rs202126703	0.00002
NM_005359.6(SMAD4):c.342T>C (p.Tyr114=)	rs757211048	0.00002
NM_005359.6(SMAD4):c.369T>C (p.Cys123=)	rs140926102	0.00002
NM_005359.6(SMAD4):c.667+3G>A	rs757971589	0.00002
NM_005359.6(SMAD4):c.1005A>G (p.Val335=)	rs878854762	0.00001
NM_005359.6(SMAD4):c.1059C>T (p.Tyr353=)	rs863224400	0.00001
NM_005359.6(SMAD4):c.1098A>G (p.Gln366=)	rs990054989	0.00001
NM_005359.6(SMAD4):c.1263A>G (p.Ala421=)	rs1406947861	0.00001
NM_005359.6(SMAD4):c.1353G>A (p.Ala451=)	rs1441353791	0.00001
NM_005359.6(SMAD4):c.1371A>G (p.Ala457=)	rs750933193	0.00001
NM_005359.6(SMAD4):c.1422A>C (p.Ser474=)	rs786201261	0.00001
NM_005359.6(SMAD4):c.1492T>C (p.Leu498=)	rs1057520520	0.00001
NM_005359.6(SMAD4):c.150A>G (p.Lys50=)	rs749503989	0.00001
NM_005359.6(SMAD4):c.160T>C (p.Leu54=)	rs1053158497	0.00001
NM_005359.6(SMAD4):c.249+10A>C	rs752243771	0.00001
NM_005359.6(SMAD4):c.276T>C (p.His92=)	rs762501162	0.00001
NM_005359.6(SMAD4):c.336T>A (p.Val112=)	rs1328102060	0.00001
NM_005359.6(SMAD4):c.375T>C (p.Ser125=)	rs863224401	0.00001
NM_005359.6(SMAD4):c.387T>C (p.Asn129=)	rs150229208	0.00001
NM_005359.6(SMAD4):c.390A>G (p.Pro130=)	rs755862230	0.00001
NM_005359.6(SMAD4):c.399C>T (p.Tyr133=)	rs779069779	0.00001
NM_005359.6(SMAD4):c.39T>C (p.Asn13=)	rs376371717	0.00001
NM_005359.6(SMAD4):c.408T>C (p.Val136=)	rs1283790116	0.00001
NM_005359.6(SMAD4):c.449G>A (p.Ser150Asn)	rs750355699	0.00001
NM_005359.6(SMAD4):c.474G>A (p.Val158=)	rs749594930	0.00001
NM_005359.6(SMAD4):c.594A>C (p.Pro198=)	rs547278031	0.00001
NM_005359.6(SMAD4):c.672G>A (p.Gln224=)	rs1397172791	0.00001
NM_005359.6(SMAD4):c.693C>T (p.Gly231=)	rs765597059	0.00001
NM_005359.6(SMAD4):c.768G>A (p.Gln256=)	rs755677513	0.00001
NM_005359.6(SMAD4):c.789C>T (p.Asn263=)	rs763510526	0.00001
NM_005359.6(SMAD4):c.855C>T (p.Asn285=)	rs1187796771	0.00001
NM_005359.6(SMAD4):c.870C>T (p.His290=)	rs1060504029	0.00001
NM_005359.6(SMAD4):c.876G>A (p.Pro292=)	rs753358186	0.00001
NM_005359.6(SMAD4):c.888C>G (p.Pro296=)	rs1060504026	0.00001
NM_005359.6(SMAD4):c.894C>T (p.Pro298=)	rs781519690	0.00001
NM_005359.6(SMAD4):c.*1G>C	rs1555687622
NM_005359.6(SMAD4):c.1081C>T (p.Arg361Cys)	rs80338963
NM_005359.6(SMAD4):c.1101C>A (p.Leu367=)	rs765051479
NM_005359.6(SMAD4):c.1206T>A (p.Leu402=)	rs758696549
NM_005359.6(SMAD4):c.1231_1232del (p.Ser411fs)	rs730881952
NM_005359.6(SMAD4):c.1245_1248del (p.Asp415Glufs)	rs80338965
NM_005359.6(SMAD4):c.1248A>G (p.Arg416=)	rs786202472
NM_005359.6(SMAD4):c.1257G>C (p.Gly419=)	rs1303474905
NM_005359.6(SMAD4):c.1309G>A (p.Val437Ile)	rs1568211172
NM_005359.6(SMAD4):c.1311C>G (p.Val437=)	rs751539807
NM_005359.6(SMAD4):c.1380C>T (p.Ala460=)	rs1910480314
NM_005359.6(SMAD4):c.1479T>C (p.Asp493=)	rs1568211528
NM_005359.6(SMAD4):c.1494A>G (p.Leu498=)	rs772479430
NM_005359.6(SMAD4):c.1512T>C (p.Ser504=)	rs1599205322
NM_005359.6(SMAD4):c.1533G>A (p.Pro511=)	rs1057523968
NM_005359.6(SMAD4):c.1545A>G (p.Arg515=)	rs760840557
NM_005359.6(SMAD4):c.1549_1550del (p.Ser517fs)	rs377767373
NM_005359.6(SMAD4):c.1595C>A (p.Ala532Asp)	rs1568211604
NM_005359.6(SMAD4):c.1599C>G (p.Leu533=)	rs2144479407
NM_005359.6(SMAD4):c.1606C>T (p.Leu536=)	rs587780790
NM_005359.6(SMAD4):c.168T>A (p.Ser56=)	rs1333506128
NM_005359.6(SMAD4):c.177A>G (p.Thr59=)	rs774480995
NM_005359.6(SMAD4):c.21G>T (p.Thr7=)	rs142292491
NM_005359.6(SMAD4):c.264A>G (p.Lys88=)	rs1555685155
NM_005359.6(SMAD4):c.298A>C (p.Arg100=)	rs751154230
NM_005359.6(SMAD4):c.507G>A (p.Gln169=)	rs876659426
NM_005359.6(SMAD4):c.513G>A (p.Ser171=)	rs1210446538
NM_005359.6(SMAD4):c.522T>C (p.Thr174=)	rs2144418435
NM_005359.6(SMAD4):c.570A>G (p.Ala190=)	rs200717327
NM_005359.6(SMAD4):c.591C>T (p.Thr197=)	rs1464524083
NM_005359.6(SMAD4):c.609A>G (p.Pro203=)	rs2144419276
NM_005359.6(SMAD4):c.633T>C (p.Thr211=)	rs1060504027
NM_005359.6(SMAD4):c.664A>G (p.Thr222Ala)	rs770461626
NM_005359.6(SMAD4):c.711G>T (p.Leu237=)	rs2144426991
NM_005359.6(SMAD4):c.756A>G (p.Gly252=)	rs1244121412
NM_005359.6(SMAD4):c.788-9A>C	rs775484792
NM_005359.6(SMAD4):c.792C>T (p.Ser264=)	rs1555685951
NM_005359.6(SMAD4):c.812G>A (p.Ser271Asn)	rs1343555503
NM_005359.6(SMAD4):c.816G>A (p.Arg272=)	rs1231028123
NM_005359.6(SMAD4):c.909T>C (p.Pro303=)	rs141149381
NM_005359.6(SMAD4):c.909T>G (p.Pro303=)	rs141149381
NM_005359.6(SMAD4):c.915C>T (p.His305=)	rs1909959040
NM_005359.6(SMAD4):c.921G>A (p.Glu307=)	rs876660255
NM_005359.6(SMAD4):c.924T>C (p.Leu308=)	rs864622414

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