Variants with conflicting interpretations studied for Disseminated atypical mycobacterial infection

Minimum review status of the submission for Disseminated atypical mycobacterial infection:		Collection method of the submission for Disseminated atypical mycobacterial infection:
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
242	24	0	9	1	1	0	11

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
Disseminated atypical mycobacterial infection		pathogenic	likely benign	benign	protective
	likely pathogenic	1	0	0	0
	uncertain significance	0	1	0	0
	likely benign	0	0	2	0
	benign	0	6	0	1

Condition to condition summary #

Total conditions: 5

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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 category conflict (e.g. benign vs affects)	Variants with any conflict
not specified	8	4	0	0	4
IFNGR1-related condition	6	2	1	0	3
Interferon gamma receptor deficiency	1	3	0	0	3
not provided	18	3	0	0	3
Mycobacterium tuberculosis, protection against	0	0	0	1	1

All variants with conflicting interpretations #

Total variants: 11

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HGVS	dbSNP	gnomAD frequency
NM_000416.3(IFNGR1):c.-56T>C	rs2234711	0.42896
NM_000416.3(IFNGR1):c.489C>T (p.Pro163=)	rs41288981	0.00668
NM_000416.3(IFNGR1):c.42G>A (p.Val14=)	rs17181471	0.00633
NM_000416.3(IFNGR1):c.1004A>C (p.His335Pro)	rs17175350	0.00438
NM_000416.3(IFNGR1):c.216A>G (p.Glu72=)	rs141574133	0.00216
NM_000416.3(IFNGR1):c.1341C>T (p.Thr447=)	rs41288979	0.00151
NM_000416.3(IFNGR1):c.538G>A (p.Gly180Arg)	rs137854904	0.00142
NM_000416.3(IFNGR1):c.1101G>A (p.Pro367=)	rs149761943	0.00131
NM_000416.3(IFNGR1):c.135C>T (p.Ile45=)	rs148104171	0.00004
NM_000416.3(IFNGR1):c.260T>C (p.Ile87Thr)	rs104893973	0.00001
NM_000416.3(IFNGR1):c.85+5C>T	rs371150014

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