ClinVar Miner

Variants with conflicting interpretations studied for Spastic paraplegia 3

Coded as:
Minimum review status of the submission for Spastic paraplegia 3: Y axis collection method of the submission for Spastic paraplegia 3:
Minimum review status of the other submission: Collection method of the other submission:
Minimum conflict level:
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 Variants with at least 2 submissions 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 kind of conflict
52 7 6 15 1 0 2 22

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
Spastic paraplegia 3 pathogenic likely pathogenic likely benign
pathogenic 6 6 0
likely pathogenic 2 0 0
uncertain significance 2 0 1
benign 0 0 9

Condition to condition summary #

Total conditions: 7
Download table as spreadsheet
Condition Variants with only 1 submission Variants with at least 2 submissions 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 kind of conflict
Spastic paraplegia 3 73 1 6 2 0 0 0 7
Spastic paraplegia, autosomal dominant 0 2 0 7 0 0 0 7
not provided 0 6 2 2 0 0 1 5
not specified 0 7 0 3 1 0 0 4
Inborn genetic diseases 0 0 0 2 0 0 0 2
Hereditary sensory neuropathy type 1D 0 0 0 0 0 0 1 1
Spastic paraplegia 3; Hereditary sensory neuropathy type 1D 0 1 1 0 0 0 0 1

All variants with conflicting interpretations #

Total variants: 22
Download table as spreadsheet
HGVS dbSNP
NM_015915.4(ATL1):c.1222A>G (p.Met408Val) rs28939094
NM_015915.4(ATL1):c.1243C>T (p.Arg415Trp) rs119476050
NM_015915.4(ATL1):c.1244G>A (p.Arg415Gln) rs397514712
NM_015915.4(ATL1):c.1483C>T (p.Arg495Trp) rs864622269
NM_015915.4(ATL1):c.196G>C (p.Glu66Gln) rs200314808
NM_015915.4(ATL1):c.351G>A (p.Glu117=) rs1060197
NM_015915.4(ATL1):c.408T>C (p.Asp136=) rs76375909
NM_015915.4(ATL1):c.417+3A>G rs200310890
NM_015915.4(ATL1):c.467C>T (p.Thr156Ile) rs137852657
NM_015915.4(ATL1):c.470T>G (p.Leu157Trp) rs119476051
NM_015915.4(ATL1):c.478T>C (p.Ser160Pro) rs886041897
NM_015915.4(ATL1):c.621G>A (p.Lys207=) rs35629585
NM_015915.4(ATL1):c.650G>A (p.Arg217Gln) rs119476049
NM_015915.4(ATL1):c.669C>T (p.Tyr223=) rs146975855
NM_015915.4(ATL1):c.693T>C (p.Gly231=) rs139720661
NM_015915.4(ATL1):c.705C>T (p.Phe235=) rs35044504
NM_015915.4(ATL1):c.715C>T (p.Arg239Cys) rs119476046
NM_015915.4(ATL1):c.757G>A (p.Val253Ile) rs864622520
NM_015915.4(ATL1):c.773A>G (p.His258Arg) rs119476048
NM_015915.4(ATL1):c.84A>G (p.Pro28=) rs35014209
NM_015915.4(ATL1):c.990+4T>A rs372029461
NM_015915.4(ATL1):c.991-6T>G rs192428744

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