Variants with conflicting interpretations studied for Lynch-like syndrome

Minimum review status of the submission for Lynch-like syndrome:		Collection method of the submission for Lynch-like 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)
		ClinVar version:

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
83	41	0	6	1	0	10	16

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
Lynch-like syndrome		pathogenic	likely pathogenic	uncertain significance	likely benign
	pathogenic	0	5	5	0
	likely pathogenic	1	0	5	0
	uncertain significance	0	0	0	1

Condition to condition summary #

Total conditions: 3

Download table as spreadsheet

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
not provided	41	6	1	9	15
not specified	5	0	1	4	5
Hereditary cancer	0	0	1	0	1

All variants with conflicting interpretations #

Total variants: 16

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HGVS	dbSNP	gnomAD frequency
NM_000535.7(PMS2):c.1004A>G (p.Asn335Ser)	rs200513014	0.00026
NM_000179.3(MSH6):c.1730G>A (p.Arg577His)	rs376220212	0.00009
NM_000179.3(MSH6):c.1483C>T (p.Arg495Ter)	rs587779212
NM_000179.3(MSH6):c.2555AGA[2] (p.Lys854del)	rs587782858
NM_000179.3(MSH6):c.2677_2678del (p.Leu893fs)	rs1572728112
NM_000179.3(MSH6):c.3416dup (p.Lys1140fs)	rs587781544
NM_000179.3(MSH6):c.3724_3726del (p.Arg1242del)	rs63749942
NM_000179.3(MSH6):c.3964G>T (p.Glu1322Ter)	rs1553333707
NM_000249.4(MLH1):c.588del (p.Lys196fs)	rs63751653
NM_000249.4(MLH1):c.676C>T (p.Arg226Ter)	rs63751615
NM_000249.4(MLH1):c.677G>T (p.Arg226Leu)	rs63751711
NM_000249.4(MLH1):c.790+1G>A	rs267607789
NM_000251.3(MSH2):c.1076G>C (p.Arg359Thr)	rs63751604
NM_000251.3(MSH2):c.1147C>T (p.Arg383Ter)	rs63749849
NM_000251.3(MSH2):c.2038C>T (p.Arg680Ter)	rs63749932
NM_000251.3(MSH2):c.2228C>T (p.Ser743Leu)	rs63751155

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