ClinVar Miner

Variants with conflicting interpretations studied for Lissencephaly, Recessive

Coded as:
Minimum review status of the submission for Lissencephaly, Recessive: Collection method of the submission for Lissencephaly, 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
49 12 0 9 35 0 0 44

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
Lissencephaly, Recessive uncertain significance likely benign benign
uncertain significance 0 28 19
likely benign 0 0 9
benign 1 0 0

Condition to condition summary #

Total conditions: 6
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 13 0 9 30 0 0 39
not specified 0 8 0 7 16 0 0 23
MYH11-related condition 0 2 0 0 5 0 0 5
RELN-related condition 0 0 0 0 5 0 0 5
Cardiovascular phenotype 0 3 0 2 2 0 0 4
Familial aortopathy 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 44
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_017668.3(NDE1):c.*899C>A rs79015533 0.11286
NM_002474.3(MYH11):c.3866T>C (p.Val1289Ala) rs16967510 0.03954
NM_017668.3(NDE1):c.948-5739G>A rs34839877 0.03595
NM_002474.3(MYH11):c.4401C>T (p.Tyr1467=) rs8046180 0.01019
NM_017668.3(NDE1):c.*384C>T rs193005461 0.00847
NM_017668.3(NDE1):c.948-6839G>A rs183176702 0.00636
NM_002474.3(MYH11):c.3949C>A (p.Leu1317Ile) rs141159831 0.00600
NM_017668.3(NDE1):c.*286G>A rs558625464 0.00322
NM_002474.3(MYH11):c.3928G>A (p.Val1310Met) rs7196804 0.00216
NM_002474.3(MYH11):c.5566C>T (p.Leu1856=) rs142639688 0.00150
NM_002474.3(MYH11):c.5529G>A (p.Ser1843=) rs146024732 0.00039
NM_017668.3(NDE1):c.948-6833A>G rs111858392 0.00039
NM_017668.3(NDE1):c.948-9293G>A rs374454501 0.00034
NM_002474.3(MYH11):c.5275G>A (p.Val1759Ile) rs138059405 0.00033
NM_002474.3(MYH11):c.5585G>A (p.Arg1862His) rs146228576 0.00025
NM_017668.3(NDE1):c.948-3127C>T rs181115969 0.00022
NM_017668.3(NDE1):c.948-5740C>T rs373378619 0.00019
NM_002474.3(MYH11):c.5094C>T (p.Ala1698=) rs771742318 0.00016
NM_002474.3(MYH11):c.5247G>A (p.Gln1749=) rs757501817 0.00014
NM_002474.3(MYH11):c.4095C>T (p.His1365=) rs374454281 0.00011
NM_002474.3(MYH11):c.5226G>C (p.Glu1742Asp) rs144421849 0.00009
NM_002474.3(MYH11):c.5277C>T (p.Val1759=) rs112564682 0.00009
NM_002474.3(MYH11):c.4681G>A (p.Ala1561Thr) rs138863103 0.00007
NM_017668.3(NDE1):c.948-9103C>T rs202120792 0.00006
NM_002474.3(MYH11):c.5772C>G (p.Leu1924=) rs774511118 0.00002
NM_002474.3(MYH11):c.4074C>T (p.Ala1358=) rs370519992 0.00001
NM_002474.3(MYH11):c.4899C>T (p.Ala1633=) rs760584464 0.00001
NM_001143979.2(NDE1):c.-165-12_-165-9del rs757466932
NM_005045.4(RELN):c.-24GGC[10] (p.Met1_Glu2insGlyGly) rs55656324
NM_005045.4(RELN):c.-24GGC[12] (p.Met1_Glu2insGlyGlyGlyGly) rs55656324
NM_005045.4(RELN):c.-24GGC[13] (p.Met1_Glu2insGlyGlyGlyGlyGly) rs55656324
NM_005045.4(RELN):c.-24GGC[14] (p.Met1_Glu2insGlyGlyGlyGlyGlyGly) rs55656324
NM_005045.4(RELN):c.-24GGC[15] (p.Met1_Glu2insGlyGlyGlyGlyGlyGlyGly) rs55656324
NM_005045.4(RELN):c.-24GGC[6] rs55656324
NM_005045.4(RELN):c.-24GGC[7] rs55656324
NM_005045.4(RELN):c.-24GGC[9] (p.Met1_Glu2insGly) rs55656324
NM_005045.4(RELN):c.1290-3dup rs146986040
NM_005045.4(RELN):c.5211-7dup rs34125550
NM_005045.4(RELN):c.5211-8_5211-7dup rs34125550
NM_017668.3(NDE1):c.*367T>C rs138543179
NM_017668.3(NDE1):c.*898del rs60544332
NM_017668.3(NDE1):c.*898dup rs60544332
NM_017668.3(NDE1):c.947+7069_947+7073del rs5815842
NM_017668.3(NDE1):c.948-3135C>T rs759760029

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