ClinVar Miner

Variants with conflicting interpretations studied for Hereditary spastic paraplegia 7

Coded as:
Minimum review status of the submission for Hereditary spastic paraplegia 7: Collection method of the submission for Hereditary spastic paraplegia 7:
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
570 61 0 23 28 0 12 62

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 7 pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 17 10 0 0
likely pathogenic 17 0 3 0 0
uncertain significance 10 3 0 23 5
likely benign 0 0 23 0 6
benign 0 0 5 6 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 7 570 61 0 23 28 0 12 62

All variants with conflicting interpretations #

Total variants: 62
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_003119.4(SPG7):c.1664-15C>A rs80292600 0.01888
NM_003119.4(SPG7):c.2188A>G (p.Asn730Asp) rs35749032 0.01431
NM_003119.4(SPG7):c.2295C>T (p.Asp765=) rs61747712 0.01110
NM_003119.4(SPG7):c.2280G>A (p.Pro760=) rs11559075 0.01053
NM_003119.4(SPG7):c.120G>A (p.Gly40=) rs187330648 0.00779
NM_003119.4(SPG7):c.1936+12C>T rs112379588 0.00628
NM_003119.4(SPG7):c.1457G>A (p.Arg486Gln) rs111475461 0.00551
NM_003119.4(SPG7):c.1032C>T (p.Gly344=) rs116319889 0.00450
NM_003119.4(SPG7):c.1529C>T (p.Ala510Val) rs61755320 0.00361
NM_003119.4(SPG7):c.987+19G>A rs62071462 0.00263
NM_003119.4(SPG7):c.4G>A (p.Ala2Thr) rs535030441 0.00136
NM_003119.4(SPG7):c.1045G>A (p.Gly349Ser) rs141659620 0.00103
NM_003119.4(SPG7):c.1083G>A (p.Ala361=) rs114135540 0.00089
NM_003119.4(SPG7):c.1324+10C>T rs202070075 0.00073
NM_003119.4(SPG7):c.1933T>A (p.Ser645Thr) rs2099104 0.00073
NM_003119.4(SPG7):c.199C>T (p.Leu67=) rs148315471 0.00066
NM_003119.4(SPG7):c.2275G>A (p.Ala759Thr) rs140769107 0.00061
NM_003119.4(SPG7):c.1359G>A (p.Ala453=) rs115448299 0.00024
NM_003119.4(SPG7):c.220G>A (p.Gly74Arg) rs114854791 0.00022
NM_003119.4(SPG7):c.233T>A (p.Leu78Ter) rs121918358 0.00014
NM_003119.4(SPG7):c.2274C>T (p.Ile758=) rs147302322 0.00011
NM_003119.4(SPG7):c.1971C>T (p.Ile657=) rs140356355 0.00009
NM_003119.4(SPG7):c.454A>G (p.Met152Val) rs146186857 0.00009
NM_003119.4(SPG7):c.2083C>G (p.Leu695Val) rs754203248 0.00008
NM_003119.4(SPG7):c.306C>T (p.Asn102=) rs147397994 0.00007
NM_003119.4(SPG7):c.1236G>A (p.Ala412=) rs201129878 0.00006
NM_003119.4(SPG7):c.1325-6C>T rs371986686 0.00006
NM_003119.4(SPG7):c.2228T>C (p.Ile743Thr) rs752623413 0.00006
NM_003119.4(SPG7):c.1266C>T (p.Ser422=) rs767857665 0.00004
NM_003119.4(SPG7):c.184-4T>C rs533778042 0.00004
NM_003119.4(SPG7):c.1948G>A (p.Asp650Asn) rs769602042 0.00004
NM_003119.4(SPG7):c.2096dup (p.Met699fs) rs747503698 0.00004
NM_003119.4(SPG7):c.656T>C (p.Ile219Thr) rs114255772 0.00004
NM_003119.4(SPG7):c.861+2dup rs771256761 0.00004
NM_003119.4(SPG7):c.637C>T (p.Arg213Ter) rs774774648 0.00003
NM_003119.4(SPG7):c.663G>A (p.Lys221=) rs575421836 0.00003
NM_003119.4(SPG7):c.201del (p.Leu67_Leu68insTer) rs763413730 0.00002
NM_003119.4(SPG7):c.619-7C>A rs779835775 0.00002
NM_003119.4(SPG7):c.1408C>T (p.Arg470Ter) rs748555510 0.00001
NM_003119.4(SPG7):c.1409G>A (p.Arg470Gln) rs756535079 0.00001
NM_003119.4(SPG7):c.1664-11C>A rs574656941 0.00001
NM_003119.4(SPG7):c.1730G>A (p.Gly577Asp) rs1329063851 0.00001
NM_003119.4(SPG7):c.1972G>A (p.Ala658Thr) rs2058661391 0.00001
NM_003119.4(SPG7):c.2271del (p.Met757fs) rs1217391623 0.00001
NM_003119.4(SPG7):c.2373G>A (p.Pro791=) rs768453376 0.00001
NM_003119.4(SPG7):c.415C>T (p.Arg139Ter) rs370777371 0.00001
NM_003119.4(SPG7):c.618+14C>T rs574361328 0.00001
NM_003119.4(SPG7):c.861+1G>C rs1412575396 0.00001
NM_003119.3(SPG7):c.1454_1462delGGCGGGAGA (p.Arg485_Glu487del) rs768823392
NM_003119.4(SPG7):c.1033G>C (p.Ala345Pro) rs368373840
NM_003119.4(SPG7):c.1169T>C (p.Val390Ala) rs2058357964
NM_003119.4(SPG7):c.1186G>T (p.Glu396Ter) rs2058358241
NM_003119.4(SPG7):c.1231G>A (p.Asp411Asn) rs745444834
NM_003119.4(SPG7):c.1324+2T>G rs1597635592
NM_003119.4(SPG7):c.1763C>T (p.Thr588Met) rs778387199
NM_003119.4(SPG7):c.1904C>T (p.Ser635Leu) rs864622507
NM_003119.4(SPG7):c.1923C>T (p.Asn641=)
NM_003119.4(SPG7):c.1967G>C (p.Arg656Pro) rs373143136
NM_003119.4(SPG7):c.2102A>C (p.His701Pro)
NM_003119.4(SPG7):c.2161A>G (p.Asn721Asp) rs2152412388
NM_003119.4(SPG7):c.759-11_759-8del rs758385553
NM_003119.4(SPG7):c.763C>T (p.Leu255=) rs2058311848

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