ClinVar Miner

Variants with conflicting interpretations studied for Hereditary spastic paraplegia

Coded as:
Minimum review status of the submission for Hereditary spastic paraplegia: Y axis collection method of the submission for Hereditary spastic paraplegia:
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
57 19 1 10 10 0 7 23

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
Hereditary spastic paraplegia pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 1 10 5 0 0
likely pathogenic 1 0 1 0 0
uncertain significance 0 2 0 10 5

Condition to condition summary #

Total conditions: 23
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
not provided 0 8 0 7 5 0 0 12
not specified 0 2 0 0 7 0 1 8
Ataxia, spastic, 2, autosomal recessive 0 1 0 0 3 0 1 3
Spastic ataxia Charlevoix-Saguenay type 0 1 0 0 1 0 1 2
Spastic paraplegia 0 4 0 0 2 0 0 2
Spastic paraplegia 11, autosomal recessive 0 1 1 1 1 0 0 2
Spastic paraplegia 46, autosomal recessive 0 0 0 2 0 0 0 2
Spastic paraplegia 7 0 2 0 2 0 0 0 2
Amyotrophic lateral sclerosis type 4; Spinocerebellar ataxia autosomal recessive 1 0 1 0 0 1 0 0 1
Autosomal dominant distal hereditary motor neuropathy 0 0 0 0 1 0 0 1
Congenital Bile Acid Synthesis Defect 0 0 0 0 0 0 1 1
Distal spinal muscular atrophy 0 0 0 0 0 0 1 1
Dysarthria; Gait ataxia; Cerebral cortical atrophy; Spastic paraparesis 0 1 0 1 0 0 0 1
Hereditary spastic paraplegia 98 0 0 1 0 0 0 1
Inborn genetic diseases 0 1 0 1 0 0 0 1
Neurodegeneration; Brain iron accummulation 0 0 0 1 0 0 0 1
Optic nerve hypoplasia 0 0 0 0 0 0 1 1
Spastic Paraplegia, Recessive 0 0 0 1 0 0 0 1
Spastic paraplegia 30, autosomal recessive; Hereditary sensory and autonomic neuropathy type IIC; Mental retardation, autosomal dominant 9 0 1 0 0 0 0 1 1
Spastic paraplegia 6 0 1 0 0 1 0 0 1
Spastic paraplegia 75, autosomal recessive 0 2 0 0 1 0 0 1
Spastic paraplegia, autosomal dominant 0 0 0 0 1 0 0 1
Spinal muscular atrophy, lower extremity-predominant, 2A, autosomal dominant 0 0 0 0 1 0 0 1

All variants with conflicting interpretations #

Total variants: 23
Download table as spreadsheet
HGVS dbSNP
NM_001003800.2(BICD2):c.269A>G (p.Lys90Arg) rs61754130
NM_001256047.1(C19orf12):c.124G>A (p.Gly42Arg) rs200133991
NM_002361.4(MAG):c.452C>T (p.Ala151Val) rs144553163
NM_003119.2(SPG7):c.1529C>T rs61755320
NM_003119.3(SPG7):c.1454_1462delGGCGGGAGA (p.Arg485_Glu487del) rs768823392
NM_003119.4(SPG7):c.1447C>T (p.Gln483Ter) rs562890289
NM_003119.4(SPG7):c.376G>C (p.Glu126Gln) rs912983346
NM_004321.7(KIF1A):c.206C>T (p.Ser69Leu) rs786200949
NM_004321.7(KIF1A):c.31C>T (p.Arg11Trp) rs548204329
NM_004820.5(CYP7B1):c.1456C>T (p.Arg486Cys) rs116171274
NM_004984.4(KIF5A):c.839G>A (p.Arg280His) rs387907288
NM_006612.6(KIF1C):c.1111G>A (p.Ala371Thr) rs142056835
NM_006612.6(KIF1C):c.2299G>A (p.Gly767Arg) rs118037269
NM_006612.6(KIF1C):c.2734C>T (p.Arg912Trp) rs202232792
NM_014363.6(SACS):c.13717A>C (p.Asn4573His) rs34382952
NM_014363.6(SACS):c.1373C>T (p.Thr458Ile) rs61729954
NM_014363.6(SACS):c.5629C>T (p.Arg1877Ter) rs761089024
NM_015046.7(SETX):c.3229G>A (p.Asp1077Asn) rs145097270
NM_020944.3(GBA2):c.1888C>T (p.Arg630Trp) rs398123012
NM_020944.3(GBA2):c.2618G>A (p.Arg873His) rs398123015
NM_025137.4(SPG11):c.3818A>G (p.Lys1273Arg) rs76389165
NM_025137.4(SPG11):c.733_734del (p.Met245fs) rs312262720
NM_144599.5(NIPA1):c.24_26GGC[10] (p.Ala15_Ala16dup) rs531550505

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