ClinVar Miner

Variants with conflicting interpretations studied for Intellectual Disability, Recessive

Coded as:
Minimum review status of the submission for Intellectual Disability, Recessive: Collection method of the submission for Intellectual Disability, Recessive:
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
28 19 0 16 32 0 0 48

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
Intellectual Disability, Recessive likely benign benign
uncertain significance 31 12
likely benign 0 11
benign 5 0

Condition to condition summary #

Total conditions: 3
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
not provided 0 23 0 11 32 0 0 43
not specified 0 14 0 12 10 0 0 22
TRAPPC9-related disorder 0 1 0 1 7 0 0 8

All variants with conflicting interpretations #

Total variants: 48
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_001160372.4(TRAPPC9):c.207T>C (p.Gly69=) rs3735801 0.55959
NM_001160372.4(TRAPPC9):c.288T>C (p.Phe96=) rs3735802 0.55845
NM_001160372.4(TRAPPC9):c.411C>T (p.Asn137=) rs3735803 0.45974
NM_001160372.4(TRAPPC9):c.1692C>T (p.Asn564=) rs12549048 0.22639
NM_003619.4(PRSS12):c.1816G>T (p.Ala606Ser) rs28661939 0.14124
NM_001160372.4(TRAPPC9):c.2292C>T (p.Gly764=) rs11166965 0.10684
NM_001160372.4(TRAPPC9):c.399T>C (p.Ala133=) rs61739560 0.08885
NM_001160372.4(TRAPPC9):c.555G>A (p.Lys185=) rs57593250 0.08881
NM_001160372.4(TRAPPC9):c.357G>A (p.Gly119=) rs34457678 0.08878
NM_001160372.4(TRAPPC9):c.2799= (p.Gly933=) rs2614718 0.08065
NM_017755.6(NSUN2):c.1602-17_1602-15del rs139131959 0.01987
NM_017755.5(NSUN2):c.-193G>C rs8192123 0.01707
NM_017755.5(NSUN2):c.-340C>T rs147269098 0.01704
NM_017755.5(NSUN2):c.-189C>A rs8192122 0.01396
NM_001160372.4(TRAPPC9):c.2742C>T (p.Thr914=) rs28710457 0.01086
NM_001160372.4(TRAPPC9):c.1869C>T (p.Ser623=) rs117685875 0.01001
NM_001160372.4(TRAPPC9):c.414C>T (p.Tyr138=) rs115986561 0.00912
NM_001160372.4(TRAPPC9):c.1458C>T (p.Phe486=) rs34179337 0.00827
NM_001160372.4(TRAPPC9):c.2797G>A (p.Gly933Ser) rs114949291 0.00641
NM_001160372.4(TRAPPC9):c.3163G>A (p.Val1055Ile) rs35578974 0.00512
NM_001160372.4(TRAPPC9):c.3249C>T (p.Phe1083=) rs112551069 0.00501
NM_001160372.4(TRAPPC9):c.588T>C (p.His196=) rs61736350 0.00284
NM_001160372.4(TRAPPC9):c.3291C>T (p.Ser1097=) rs148857575 0.00222
NM_001160372.4(TRAPPC9):c.1407C>T (p.Tyr469=) rs117632905 0.00151
NM_001160372.4(TRAPPC9):c.1164C>T (p.Tyr388=) rs148976893 0.00136
NM_001160372.4(TRAPPC9):c.3149G>A (p.Arg1050Gln) rs111768745 0.00103
NM_001160372.4(TRAPPC9):c.3414T>G (p.Ser1138Arg) rs147127279 0.00089
NM_001160372.4(TRAPPC9):c.263C>T (p.Ser88Leu) rs139631202 0.00072
NM_001160372.4(TRAPPC9):c.3175G>A (p.Ala1059Thr) rs150200902 0.00056
NM_001160372.4(TRAPPC9):c.2796C>T (p.Ala932=) rs145607512 0.00038
NM_031466.8(TRAPPC9):c.-135A>G rs148523016 0.00037
NM_001160372.4(TRAPPC9):c.1809G>A (p.Leu603=) rs146235874 0.00029
NM_001160372.4(TRAPPC9):c.3411C>A (p.Pro1137=) rs373979305 0.00022
NM_001160372.4(TRAPPC9):c.370A>G (p.Ile124Val) rs117688394 0.00022
NM_001160372.4(TRAPPC9):c.3136C>T (p.Arg1046Trp) rs376617920 0.00015
NM_031466.8(TRAPPC9):c.-24G>A rs370984854 0.00009
NM_001160372.4(TRAPPC9):c.2245C>T (p.Leu749=) rs375545861 0.00006
NM_001160372.4(TRAPPC9):c.2793C>T (p.His931=) rs886062722 0.00004
NM_001160372.4(TRAPPC9):c.3288G>A (p.Pro1096=) rs570688248 0.00003
NM_001160372.4(TRAPPC9):c.2988G>A (p.Glu996=) rs142048892 0.00002
NM_001160372.4(TRAPPC9):c.1560C>T (p.Pro520=) rs886062724 0.00001
NM_001160372.4(TRAPPC9):c.*532G>A rs187594197
NM_001160372.4(TRAPPC9):c.1326G>A (p.Ser442=) rs145960296
NM_001160372.4(TRAPPC9):c.2279-11del rs758850777
NM_001160372.4(TRAPPC9):c.2475G>A (p.Arg825=) rs756688439
NM_001160372.4(TRAPPC9):c.3225C>T (p.Tyr1075=) rs58740567
NM_017755.5(NSUN2):c.-217delT rs8192124
NM_017755.5(NSUN2):c.-73C>T rs139145592

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