ClinVar Miner

Variants with conflicting interpretations studied for Hereditary spastic paraplegia 4

Coded as:
Minimum review status of the submission for Hereditary spastic paraplegia 4: Collection method of the submission for Hereditary spastic paraplegia 4:
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 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
869 66 0 34 9 1 14 54

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 4 pathogenic likely pathogenic uncertain significance likely benign benign risk factor
pathogenic 0 22 9 0 0 0
likely pathogenic 22 0 5 1 0 0
uncertain significance 9 5 0 9 2 0
likely benign 0 1 9 0 12 1
benign 0 0 2 12 0 1
risk factor 0 0 0 1 1 0

Condition to condition summary #

Total conditions: 1
Download table as spreadsheet
Condition 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
Hereditary spastic paraplegia 4 869 66 0 34 9 1 14 54

All variants with conflicting interpretations #

Total variants: 54
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_014946.4(SPAST):c.131C>T (p.Ser44Leu) rs121908515 0.00521
NM_014946.4(SPAST):c.484G>A (p.Val162Ile) rs141944844 0.00192
NM_014946.4(SPAST):c.415+12G>A rs539075273 0.00115
NM_014946.4(SPAST):c.134C>A (p.Pro45Gln) rs121908517 0.00063
NM_014946.4(SPAST):c.683-9C>T rs202209866 0.00056
NM_014946.4(SPAST):c.1493+6G>A rs115659052 0.00046
NM_014946.4(SPAST):c.1735A>C (p.Asn579His) rs144594804 0.00031
NM_014946.4(SPAST):c.289C>A (p.Pro97Thr) rs372005558 0.00029
NM_014946.4(SPAST):c.1625A>G (p.Asp542Gly) rs142053576 0.00024
NM_014946.4(SPAST):c.1593A>G (p.Gln531=) rs754291673 0.00023
NM_014946.4(SPAST):c.30G>A (p.Lys10=) rs768928614 0.00005
NM_014946.4(SPAST):c.441A>G (p.Glu147=) rs375027118 0.00004
NM_014946.4(SPAST):c.631G>A (p.Val211Ile) rs143003434 0.00002
NM_014946.4(SPAST):c.828T>C (p.Ser276=) rs77525846 0.00002
NM_014946.4(SPAST):c.878C>T (p.Pro293Leu) rs773193617 0.00002
NM_014946.4(SPAST):c.137A>G (p.His46Arg) rs778952334 0.00001
NM_014946.4(SPAST):c.1685G>A (p.Arg562Gln) rs863224923 0.00001
NM_014946.4(SPAST):c.1817G>A (p.Arg606His) rs768077366 0.00001
NM_014946.4(SPAST):c.626C>T (p.Thr209Met) rs537855621 0.00001
NM_014946.4(SPAST):c.1103T>C (p.Phe368Ser) rs1553316799
NM_014946.4(SPAST):c.1173G>A (p.Leu391=) rs1679218212
NM_014946.4(SPAST):c.1174-1G>A rs1553317024
NM_014946.4(SPAST):c.1196C>T (p.Ser399Leu) rs1553317025
NM_014946.4(SPAST):c.1216A>G (p.Ile406Val) rs587777757
NM_014946.4(SPAST):c.1245+6T>G rs1553317050
NM_014946.4(SPAST):c.1276C>T (p.Leu426Phe) rs1060502227
NM_014946.4(SPAST):c.129G>C (p.Glu43Asp) rs542793579
NM_014946.4(SPAST):c.1307C>T (p.Ser436Phe) rs1553318184
NM_014946.4(SPAST):c.1340T>C (p.Leu447Ser) rs2148753950
NM_014946.4(SPAST):c.1348A>G (p.Arg450Gly) rs1553318223
NM_014946.4(SPAST):c.1413+1_1413+2del rs1679558544
NM_014946.4(SPAST):c.1413+3_1413+6del rs570685843
NM_014946.4(SPAST):c.1437_1438del (p.Arg479fs) rs864622268
NM_014946.4(SPAST):c.1477G>C (p.Asp493His) rs1060499939
NM_014946.4(SPAST):c.1483G>T (p.Ala495Ser) rs1060502228
NM_014946.4(SPAST):c.1484C>T (p.Ala495Val) rs1553318347
NM_014946.4(SPAST):c.1496G>A (p.Arg499His) rs878854991
NM_014946.4(SPAST):c.1507C>T (p.Arg503Trp) rs864622162
NM_014946.4(SPAST):c.1537-11A>G rs549538513
NM_014946.4(SPAST):c.1550T>C (p.Leu517Ser) rs2148759388
NM_014946.4(SPAST):c.1553T>C (p.Leu518Pro) rs1553319290
NM_014946.4(SPAST):c.1616+1G>A rs1553319327
NM_014946.4(SPAST):c.1616+5G>A rs2148759485
NM_014946.4(SPAST):c.1676G>A (p.Gly559Asp) rs864622179
NM_014946.4(SPAST):c.1715T>C (p.Met572Thr) rs138146982
NM_014946.4(SPAST):c.1742G>C (p.Arg581Pro) rs749484350
NM_014946.4(SPAST):c.1744T>C (p.Leu582=) rs886055962
NM_014946.4(SPAST):c.1774del (p.Lys591_Ile592insTer) rs1680185365
NM_014946.4(SPAST):c.1775T>A (p.Ile592Lys) rs1553321237
NM_014946.4(SPAST):c.1841C>T (p.Thr614Ile) rs1573186691
NM_014946.4(SPAST):c.1849T>G (p.Ter617Glu) rs1553321270
NM_014946.4(SPAST):c.302C>A (p.Ser101Ter) rs746263735
NM_014946.4(SPAST):c.519A>G (p.Arg173=) rs1677627735
NM_014946.4(SPAST):c.67_85dup (p.Leu29fs) rs1676388641

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