Variants with conflicting interpretations studied for Intellectual disability

Minimum review status of the submission for Intellectual disability:		Collection method of the submission for Intellectual disability:
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
2497	12	0	7	1	0	3	10

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
Intellectual disability		pathogenic	likely pathogenic	uncertain significance	likely benign
	pathogenic	0	7	1	0
	likely pathogenic	5	0	3	0
	uncertain significance	1	3	0	1
	likely benign	0	0	1	0

Condition to condition summary #

Total conditions: 4

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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
Intellectual disability	2501	10	5	1	3	8
Seizure; Intellectual disability	0	1	2	0	1	2
Global developmental delay; Seizure; Intellectual disability	0	0	1	0	1	1
Hirsutism; Intellectual disability	0	0	1	0	0	1

All variants with conflicting interpretations #

Total variants: 10

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HGVS	dbSNP	gnomAD frequency
NM_001371986.1(UNC80):c.1806G>C (p.Gln602His)	rs200473652	0.00163
NM_000314.8(PTEN):c.269T>C (p.Phe90Ser)	rs1859965098	0.00001
NM_001244008.2(KIF1A):c.4648C>T (p.Arg1550Trp)	rs1468401006	0.00001
NM_000489.6(ATRX):c.109C>T (p.Arg37Ter)	rs122445108
NM_001032221.6(STXBP1):c.416C>T (p.Pro139Leu)	rs796053353
NM_001352027.3(PHF21A):c.1741C>T (p.Arg581Ter)
NM_001366145.2(TRPM3):c.3004G>A (p.Val1002Met)	rs1564493599
NM_003070.5(SMARCA2):c.3602C>T (p.Ala1201Val)	rs281875189
NM_004519.4(KCNQ3):c.688C>T (p.Arg230Cys)	rs796052676
Single allele

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