Variants with conflicting interpretations studied for Rare genetic intellectual disability

Minimum review status of the submission for Rare genetic intellectual disability:		Collection method of the submission for Rare genetic 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
32	11	0	10	2	0	2	14

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
Rare genetic intellectual disability		pathogenic	likely pathogenic	uncertain significance	likely benign
	pathogenic	0	1	0	0
	likely pathogenic	9	0	2	0
	uncertain significance	0	0	0	2

Condition to condition summary #

Total conditions: 3

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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	11	10	2	2	14
KANK1-related condition	0	0	1	0	1
Spastic paraplegia	0	1	0	0	1

All variants with conflicting interpretations #

Total variants: 14

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HGVS	dbSNP	gnomAD frequency
NM_015158.5(KANK1):c.3772G>T (p.Ala1258Ser)	rs113362230	0.00019
NM_133379.5(TTN):c.16282G>A (p.Val5428Met)	rs199565262	0.00010
NM_001099922.3(ALG13):c.320A>G (p.Asn107Ser)	rs398122394
NM_001349338.3(FOXP1):c.1321_1324del (p.Asp441fs)
NM_001356.5(DDX3X):c.454dup (p.Ser152fs)
NM_001374828.1(ARID1B):c.6895del (p.Gln2299fs)	rs1794569741
NM_004187.5(KDM5C):c.3392_3393del (p.Glu1131fs)
NM_004380.3(CREBBP):c.6241C>T (p.Gln2081Ter)	rs886041518
NM_006009.4(TUBA1A):c.1168C>T (p.Arg390Cys)	rs1064793286
NM_013275.6(ANKRD11):c.3369_3372del (p.Ser1123fs)
NM_013275.6(ANKRD11):c.3770_3771del (p.Lys1257fs)	rs886039477
NM_015335.5(MED13L):c.2333C>T (p.Ala778Val)	rs1555247422
NM_016628.5(WAC):c.451C>T (p.Arg151Ter)	rs886041614
NM_017934.7(PHIP):c.2854C>T (p.Arg952Ter)

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