ClinVar Miner

Variants in gene combination SCN1A, SCN9A with conflicting interpretations

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Y axis minimum submission review status: Y axis collection method:
X axis minimum submission review status: X axis collection method:
Minimum conflict level:
Gene type:
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
2162 118 0 38 38 0 4 73

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.

pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 3 2 1 0
likely pathogenic 3 0 2 0 0
uncertain significance 2 2 0 35 6
likely benign 1 0 35 0 35
benign 0 0 6 35 0

All variants with conflicting interpretations #

Total variants: 73
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_001365536.1(SCN9A):c.1287T>A (p.Arg429=) rs6747673 0.56670
NM_001365536.1(SCN9A):c.1266A>G (p.Glu422=) rs13402180 0.38348
NM_001365536.1(SCN9A):c.1119T>C (p.Ala373=) rs13414203 0.38341
NM_001365536.1(SCN9A):c.3802-4A>G rs75230218 0.06754
NM_001365536.1(SCN9A):c.4812G>T (p.Val1604=) rs149207258 0.06646
NM_001365536.1(SCN9A):c.1469G>A (p.Ser490Asn) rs58022607 0.04393
NM_001365536.1(SCN9A):c.1155G>T (p.Val385=) rs58465962 0.04390
NM_001365536.1(SCN9A):c.5756A>G (p.Asp1919Gly) rs3750904 0.02756
NM_001365536.1(SCN9A):c.3802-8T>C rs76550960 0.02262
NM_001365536.1(SCN9A):c.3362G>A (p.Arg1121Gln) rs74401238 0.02210
NM_001365536.1(SCN9A):c.2827A>C (p.Met943Leu) rs12478318 0.01339
NM_001365536.1(SCN9A):c.3004G>T (p.Val1002Leu) rs4369876 0.01322
NM_001365536.1(SCN9A):c.3767A>G (p.Asn1256Ser) rs141268327 0.00496
NM_001365536.1(SCN9A):c.2517+6C>T rs145316463 0.00460
NM_001365536.1(SCN9A):c.1398C>T (p.Ser466=) rs201531206 0.00386
NM_001365536.1(SCN9A):c.2190G>C (p.Trp730Cys) rs202055175 0.00341
NM_001365536.1(SCN9A):c.5779C>T (p.Leu1927Phe) rs111558968 0.00315
NM_001365536.1(SCN9A):c.3361C>T (p.Arg1121Trp) rs190664764 0.00304
NM_001365536.1(SCN9A):c.2248A>G (p.Ile750Val) rs182650126 0.00278
NM_001365536.1(SCN9A):c.4356C>T (p.Phe1452=) rs201145311 0.00263
NM_001365536.1(SCN9A):c.3506A>C (p.Asn1169Thr) rs151241025 0.00216
NM_001365536.1(SCN9A):c.1997A>G (p.Lys666Arg) rs121908919 0.00180
NM_001365536.1(SCN9A):c.3832C>G (p.Leu1278Val) rs180922748 0.00174
NM_001365536.1(SCN9A):c.4314C>T (p.Val1438=) rs188336294 0.00171
NM_001365536.1(SCN9A):c.3051G>C (p.Lys1017Asn) rs147623238 0.00149
NM_001365536.1(SCN9A):c.3675C>A (p.Ile1225=) rs77144869 0.00141
NM_001365536.1(SCN9A):c.3509T>C (p.Ile1170Thr) rs73019664 0.00128
NM_001365536.1(SCN9A):c.2409T>C (p.Tyr803=) rs142219317 0.00106
NM_001365536.1(SCN9A):c.1326G>A (p.Ala442=) rs200065104 0.00102
NM_001365536.1(SCN9A):c.3195C>T (p.Ser1065=) rs111674454 0.00099
NM_001365536.1(SCN9A):c.2766C>T (p.Arg922=) rs199653503 0.00096
NM_001365536.1(SCN9A):c.3403C>T (p.Pro1135Ser) rs184563685 0.00081
NM_001365536.1(SCN9A):c.4315G>A (p.Val1439Ile) rs149346064 0.00061
NM_001365536.1(SCN9A):c.1464C>T (p.Leu488=) rs200682458 0.00059
NM_001365536.1(SCN9A):c.1555G>A (p.Glu519Lys) rs187453572 0.00059
NM_001365536.1(SCN9A):c.2392A>G (p.Met798Val) rs149707354 0.00056
NM_001365536.1(SCN9A):c.3002A>G (p.Tyr1001Cys) rs199692186 0.00056
NM_001365536.1(SCN9A):c.3402G>T (p.Leu1134Phe) rs200160858 0.00052
NM_001365536.1(SCN9A):c.3801T>C (p.Asp1267=) rs202047865 0.00043
NM_001365536.1(SCN9A):c.4923T>C (p.Leu1641=) rs199550149 0.00041
NM_001365536.1(SCN9A):c.2005C>T (p.Arg669Cys) rs200174262 0.00038
NM_001365536.1(SCN9A):c.3684T>C (p.Tyr1228=) rs144941725 0.00035
NM_001365536.1(SCN9A):c.2964C>T (p.Leu988=) rs201430964 0.00032
NM_001365536.1(SCN9A):c.1980G>A (p.Thr660=) rs200014315 0.00023
NM_001365536.1(SCN9A):c.2192T>A (p.Ile731Lys) rs200945460 0.00019
NM_001365536.1(SCN9A):c.4110T>C (p.Cys1370=) rs199673396 0.00019
NM_001365536.1(SCN9A):c.4495C>A (p.Arg1499=) rs187558439 0.00019
NM_001365536.1(SCN9A):c.2344-20A>T rs199905079 0.00018
NM_001365536.1(SCN9A):c.1177C>T (p.Leu393=) rs184773311 0.00017
NM_001365536.1(SCN9A):c.1110G>A (p.Thr370=) rs202002028 0.00016
NM_001365536.1(SCN9A):c.3482G>A (p.Trp1161Ter) rs759003928 0.00011
NM_001365536.1(SCN9A):c.3207C>T (p.His1069=) rs200689065 0.00010
NM_001365536.1(SCN9A):c.2165T>C (p.Leu722Ser) rs187526567 0.00009
NM_001365536.1(SCN9A):c.5711G>A (p.Arg1904His) rs79805025 0.00009
NM_001365536.1(SCN9A):c.2461G>A (p.Val821Met) rs41268671 0.00006
NM_001365536.1(SCN9A):c.5379G>A (p.Ala1793=) rs201875421 0.00006
NM_001365536.1(SCN9A):c.5945A>T (p.Asp1982Val) rs199822303 0.00006
NM_001365536.1(SCN9A):c.1975-8T>A rs752961542 0.00005
NM_001365536.1(SCN9A):c.902-2A>C rs773824421 0.00005
NM_001365536.1(SCN9A):c.1793G>A (p.Arg598His) rs201318927 0.00004
NM_001365536.1(SCN9A):c.1921A>T (p.Asn641Tyr) rs121908918 0.00004
NM_001365536.1(SCN9A):c.2719C>T (p.Arg907Trp) rs202152511 0.00004
NM_001365536.1(SCN9A):c.2437A>G (p.Ser813Gly) rs201890240 0.00003
NM_001365536.1(SCN9A):c.2496A>C (p.Ser832=) rs200185692 0.00002
NM_001365536.1(SCN9A):c.1285C>T (p.Arg429Cys) rs763256222 0.00001
NM_001365536.1(SCN9A):c.1347T>C (p.Ser449=) rs201990547 0.00001
NM_001365536.1(SCN9A):c.1713C>T (p.Ala571=) rs200876333 0.00001
NM_001365536.1(SCN9A):c.2720G>A (p.Arg907Gln) rs1024152367 0.00001
NM_001365536.1(SCN9A):c.1828C>A (p.Pro610Thr) rs41268673
NM_001365536.1(SCN9A):c.1975-3del rs35888674
NM_001365536.1(SCN9A):c.2576T>C (p.Ile859Thr) rs80356474
NM_001365536.1(SCN9A):c.2874+11_2874+13delinsTT rs1553487749
NM_001365536.1(SCN9A):c.3019C>T (p.Arg1007Cys) rs121908910

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