ClinVar Miner

Variants with conflicting interpretations studied for Short-rib thoracic dysplasia 6 with or without polydactyly

Coded as:
Minimum review status of the submission for Short-rib thoracic dysplasia 6 with or without polydactyly: Collection method of the submission for Short-rib thoracic dysplasia 6 with or without polydactyly:
Minimum review status of the other submission: Collection method of the other submission:
Minimum conflict level:

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
678 31 0 31 29 0 6 65

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
Short-rib thoracic dysplasia 6 with or without polydactyly pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 24 0 0 0
likely pathogenic 24 0 6 1 0
uncertain significance 0 6 0 26 3
likely benign 0 1 26 0 7
benign 0 0 3 7 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
Short-rib thoracic dysplasia 6 with or without polydactyly 678 31 0 31 29 0 6 65

All variants with conflicting interpretations #

Total variants: 65
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_001199397.3(NEK1):c.1388C>T (p.Ala463Val) rs34540355 0.03580
NM_001199397.3(NEK1):c.2235T>G (p.Asn745Lys) rs34324114 0.00412
NM_001199397.3(NEK1):c.1021G>A (p.Ala341Thr) rs189186475 0.00227
NM_001199397.3(NEK1):c.975A>G (p.Gly325=) rs150904906 0.00218
NM_001199397.3(NEK1):c.782G>A (p.Arg261His) rs200161705 0.00216
NM_001199397.3(NEK1):c.1581T>C (p.Ala527=) rs184804243 0.00172
NM_001199397.3(NEK1):c.3411G>A (p.Leu1137=) rs56077602 0.00169
NM_001199397.3(NEK1):c.924T>G (p.Ile308Met) rs10034957 0.00151
NM_020779.4(WDR35):c.1183A>T (p.Asn395Tyr) rs143343508 0.00135
NM_001199397.3(NEK1):c.2137G>A (p.Val713Met) rs199827465 0.00064
NM_001199397.3(NEK1):c.277A>G (p.Asn93Asp) rs201350526 0.00064
NM_001199397.3(NEK1):c.686A>G (p.Tyr229Cys) rs61737748 0.00057
NM_025103.4(IFT74):c.120+2dup rs551515830 0.00046
NM_020800.3(IFT80):c.721G>C (p.Gly241Arg) rs138004478 0.00043
NM_001199397.3(NEK1):c.3567C>T (p.Asn1189=) rs200710438 0.00038
NM_153717.3(EVC):c.1886+5G>T rs794726665 0.00036
NM_001199397.3(NEK1):c.3583+8A>C rs192372022 0.00026
NM_001199397.3(NEK1):c.1617G>A (p.Gln539=) rs146569517 0.00025
NM_001199397.3(NEK1):c.912T>C (p.Pro304=) rs139433990 0.00015
NM_001199397.3(NEK1):c.642G>A (p.Lys214=) rs369725706 0.00010
NM_025129.5(FUZ):c.98_111+9del rs548706733 0.00010
NM_001199397.3(NEK1):c.2421C>T (p.Phe807=) rs56346829 0.00009
NM_001199397.3(NEK1):c.3107C>G (p.Ser1036Ter) rs199947197 0.00009
NM_024753.5(TTC21B):c.2500C>T (p.Gln834Ter) rs79746977 0.00009
NM_001199397.3(NEK1):c.2587+14G>T rs368032168 0.00008
NM_001377.3(DYNC2H1):c.10322T>C (p.Leu3441Pro) rs771487311 0.00007
NM_147127.5(EVC2):c.1708C>T (p.Gln570Ter) rs769864196 0.00005
NM_001199397.3(NEK1):c.3622G>A (p.Asp1208Asn) rs35503975 0.00004
NM_001199397.3(NEK1):c.3715-6G>C rs771507979 0.00004
NM_001199397.3(NEK1):c.1063A>G (p.Arg355Gly) rs35763578 0.00003
NM_001199397.3(NEK1):c.1226G>A (p.Trp409Ter) rs985064686 0.00003
NM_001199397.3(NEK1):c.1500T>C (p.Ala500=) rs776664093 0.00003
NM_001199397.3(NEK1):c.3135T>C (p.Ser1045=) rs370713361 0.00003
NM_147127.5(EVC2):c.1195C>T (p.Arg399Ter) rs137852924 0.00003
NM_153717.3(EVC):c.1018C>T (p.Arg340Ter) rs121908425 0.00003
NM_001199397.3(NEK1):c.214+1G>A rs1049502301 0.00002
NM_001199397.3(NEK1):c.591T>C (p.Cys197=) rs755160503 0.00002
NM_001377.3(DYNC2H1):c.10042+2T>G rs1261505725 0.00002
NM_001199397.3(NEK1):c.1427A>G (p.Glu476Gly) rs765781871 0.00001
NM_001199397.3(NEK1):c.1618C>T (p.Arg540Ter) rs758677637 0.00001
NM_001199397.3(NEK1):c.2093T>C (p.Met698Thr) rs577165880 0.00001
NM_001199397.3(NEK1):c.2136C>T (p.Gly712=) rs760404694 0.00001
NM_001199397.3(NEK1):c.2726C>G (p.Ser909Cys) rs543224510 0.00001
NM_001199397.3(NEK1):c.3075C>T (p.Asn1025=) rs886059227 0.00001
NM_001199397.3(NEK1):c.3405A>G (p.Gln1135=) rs774338352 0.00001
NM_001377.3(DYNC2H1):c.12896G>A (p.Gly4299Glu) rs770569272 0.00001
NM_015650.4(IFT54):c.169G>A (p.Glu57Lys) rs769651861 0.00001
NM_015650.4(IFT54):c.988-1G>C rs372499275 0.00001
NM_020779.4(WDR35):c.206G>A (p.Gly69Asp) rs765513105 0.00001
NM_024753.5(TTC21B):c.131C>A (p.Ala44Asp) rs1553516687 0.00001
NM_001199397.3(NEK1):c.1334A>G (p.His445Arg) rs574204412
NM_001199397.3(NEK1):c.1769_1770del (p.Arg590fs) rs1554053289
NM_001199397.3(NEK1):c.1868del (p.Ser623fs) rs1362848762
NM_001199397.3(NEK1):c.2161C>T (p.Arg721Trp) rs201726561
NM_001199397.3(NEK1):c.2241del (p.Ala750fs)
NM_001199397.3(NEK1):c.2814_2817del (p.Asn938fs) rs752878896
NM_001199397.3(NEK1):c.2886-1G>A rs773496891
NM_001199397.3(NEK1):c.2974+11T>C rs886059229
NM_001199397.3(NEK1):c.3141G>A (p.Ser1047=) rs190807750
NM_001199397.3(NEK1):c.3289G>A (p.Val1097Ile) rs374890006
NM_001199397.3(NEK1):c.599_602del (p.Lys200fs) rs1554075284
NM_001199397.3(NEK1):c.894C>G (p.Asn298Lys) rs745526568
NM_016008.4(DYNC2LI1):c.394C>A (p.Gln132Lys) rs76483206
NM_153717.3(EVC):c.363C>A (p.Tyr121Ter) rs748523193
NM_153717.3(EVC):c.901AAG[1] (p.Lys302del) rs755381180

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