ClinVar Miner

Variants with conflicting interpretations studied for MHC class II deficiency

Coded as:
Minimum review status of the submission for MHC class II deficiency: Collection method of the submission for MHC class II deficiency:
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
2253 244 0 37 100 0 2 133

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
MHC class II deficiency pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 15 1 0 0
likely pathogenic 16 0 2 0 0
uncertain significance 1 2 0 87 16
likely benign 0 0 88 0 20
benign 0 0 17 20 0

Condition to condition summary #

Total conditions: 2
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
MHC class II deficiency 2259 241 0 34 99 0 2 130
MHC class II deficiency 1 0 7 0 6 1 0 0 7

All variants with conflicting interpretations #

Total variants: 133
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000246.4(CIITA):c.2448C>T (p.Ala816=) rs112250421 0.00272
NM_000246.4(CIITA):c.53-12C>T rs112310350 0.00243
NM_000538.4(RFXAP):c.24G>A (p.Glu8=) rs540467033 0.00205
NM_003721.4(RFXANK):c.445G>A (p.Asp149Asn) rs115220304 0.00203
NM_001025603.2(RFX5):c.233+4G>C rs2233846 0.00173
NM_001025603.2(RFX5):c.1379G>A (p.Ser460Asn) rs142053610 0.00167
NM_003721.4(RFXANK):c.95C>T (p.Ala32Val) rs114064359 0.00146
NM_000538.4(RFXAP):c.756A>G (p.Gln252=) rs141918438 0.00123
NM_000246.4(CIITA):c.1461C>G (p.Ile487Met) rs141202424 0.00120
NM_000246.4(CIITA):c.460G>A (p.Asp154Asn) rs76923280 0.00098
NM_000246.4(CIITA):c.1068G>A (p.Pro356=) rs140486686 0.00081
NM_000246.4(CIITA):c.1740C>G (p.Arg580=) rs78666334 0.00070
NM_000538.4(RFXAP):c.312C>T (p.Ser104=) rs373233313 0.00056
NM_000246.4(CIITA):c.712C>T (p.His238Tyr) rs150307400 0.00050
NM_000246.4(CIITA):c.2651G>A (p.Arg884His) rs374443915 0.00048
NM_000246.4(CIITA):c.931A>G (p.Met311Val) rs140139362 0.00046
NM_003721.4(RFXANK):c.187+13C>T rs201778172 0.00044
NM_000246.4(CIITA):c.1518G>A (p.Ala506=) rs201215476 0.00043
NM_000538.4(RFXAP):c.666A>G (p.Ala222=) rs139675642 0.00043
NM_000246.4(CIITA):c.456G>A (p.Pro152=) rs151317882 0.00035
NM_000246.4(CIITA):c.1926C>T (p.Val642=) rs138376967 0.00033
NM_000246.4(CIITA):c.3150-6C>T rs192219239 0.00030
NM_003721.4(RFXANK):c.188-11C>T rs201545133 0.00029
NM_001025603.2(RFX5):c.477T>C (p.Tyr159=) rs144353639 0.00028
NM_001025603.2(RFX5):c.1569G>A (p.Glu523=) rs137968641 0.00027
NM_000246.4(CIITA):c.2817-10T>C rs75381106 0.00023
NM_000246.4(CIITA):c.2892G>A (p.Leu964=) rs200599265 0.00021
NM_000246.4(CIITA):c.1230G>A (p.Pro410=) rs199476069 0.00019
NM_000538.4(RFXAP):c.77C>G (p.Pro26Arg) rs763162669 0.00019
NM_000538.4(RFXAP):c.430G>A (p.Glu144Lys) rs201754085 0.00016
NM_000246.4(CIITA):c.1047T>C (p.Tyr349=) rs144735718 0.00013
NM_000246.4(CIITA):c.1542G>A (p.Thr514=) rs2228239 0.00013
NM_000246.4(CIITA):c.1791C>G (p.Leu597=) rs201657235 0.00013
NM_000246.4(CIITA):c.1908G>A (p.Thr636=) rs200398959 0.00013
NM_000246.4(CIITA):c.3003C>T (p.Asp1001=) rs143497260 0.00013
NM_000246.4(CIITA):c.772+8C>T rs557455283 0.00012
NM_003721.4(RFXANK):c.660C>T (p.Ala220=) rs138423094 0.00012
NM_000246.4(CIITA):c.2405G>A (p.Arg802Gln) rs201182990 0.00011
NM_003721.4(RFXANK):c.529C>G (p.Leu177Val) rs151053440 0.00011
NM_000246.4(CIITA):c.1545C>T (p.Cys515=) rs200146904 0.00010
NM_001025603.2(RFX5):c.1830C>G (p.Asp610Glu) rs141889707 0.00010
NM_000246.4(CIITA):c.1731C>T (p.Tyr577=) rs142848848 0.00009
NM_000246.4(CIITA):c.1486C>T (p.Leu496Phe) rs756970534 0.00008
NM_000246.4(CIITA):c.2384G>A (p.Arg795Gln) rs553503699 0.00008
NM_000246.4(CIITA):c.1683C>T (p.Asp561=) rs76686583 0.00007
NM_000246.4(CIITA):c.3063-12G>T rs559875711 0.00007
NM_000246.4(CIITA):c.2832G>A (p.Ser944=) rs766538754 0.00006
NM_000246.4(CIITA):c.2979G>A (p.Ala993=) rs142031278 0.00006
NM_000246.4(CIITA):c.3175G>A (p.Val1059Met) rs200742204 0.00006
NM_000246.4(CIITA):c.384C>T (p.Ile128=) rs140106499 0.00006
NM_000246.4(CIITA):c.772+5G>T rs376221650 0.00006
NM_003721.4(RFXANK):c.338-13C>G rs749579925 0.00006
NM_000246.4(CIITA):c.1006+12G>A rs368964652 0.00005
NM_000246.4(CIITA):c.1944A>T (p.Ala648=) rs778678693 0.00005
NM_000246.4(CIITA):c.1834A>G (p.Thr612Ala) rs142257962 0.00004
NM_000246.4(CIITA):c.2617T>C (p.Leu873=) rs368233530 0.00004
NM_001025603.2(RFX5):c.117-13C>T rs371670135 0.00004
NM_001025603.2(RFX5):c.807T>G (p.Gly269=) rs147137349 0.00004
NM_000246.4(CIITA):c.2409G>A (p.Ala803=) rs755302593 0.00003
NM_000246.4(CIITA):c.2442C>T (p.His814=) rs746490057 0.00003
NM_000246.4(CIITA):c.2888+1G>A rs372826934 0.00003
NM_000246.4(CIITA):c.3318-8C>G rs201115726 0.00003
NM_000246.4(CIITA):c.3357C>T (p.His1119=) rs754706834 0.00003
NM_000246.4(CIITA):c.772+9G>A rs750572482 0.00003
NM_000246.4(CIITA):c.948G>A (p.Thr316=) rs369971838 0.00003
NM_003721.4(RFXANK):c.501C>A (p.Gly167=) rs145457604 0.00003
NM_000246.4(CIITA):c.1527C>T (p.Gly509=) rs1427227633 0.00002
NM_000246.4(CIITA):c.2343G>A (p.Ser781=) rs749019138 0.00002
NM_000246.4(CIITA):c.3207G>A (p.Pro1069=) rs772387879 0.00002
NM_000538.4(RFXAP):c.127C>T (p.Gln43Ter) rs1313207845 0.00002
NM_001025603.2(RFX5):c.1797G>A (p.Val599=) rs772352167 0.00002
NM_003721.4(RFXANK):c.240C>T (p.Asn80=) rs754519730 0.00002
NM_000246.4(CIITA):c.1149C>T (p.Ala383=) rs748867171 0.00001
NM_000246.4(CIITA):c.1245G>A (p.Val415=) rs2039185777 0.00001
NM_000246.4(CIITA):c.1518del (p.Gln507fs) rs2544477641 0.00001
NM_000246.4(CIITA):c.1635C>G (p.Leu545=) rs748330320 0.00001
NM_000246.4(CIITA):c.200-9T>C rs778238111 0.00001
NM_000246.4(CIITA):c.2139G>A (p.Leu713=) rs1319022837 0.00001
NM_000246.4(CIITA):c.2142A>G (p.Gln714=) rs188988714 0.00001
NM_000246.4(CIITA):c.2256G>A (p.Glu752=) rs200577013 0.00001
NM_000246.4(CIITA):c.2709G>A (p.Gly903=) rs755515727 0.00001
NM_000246.4(CIITA):c.2816+9A>G rs2039386253 0.00001
NM_000246.4(CIITA):c.2965C>T (p.Leu989=) rs1256846733 0.00001
NM_000246.4(CIITA):c.2994G>A (p.Lys998=) rs1286058878 0.00001
NM_000246.4(CIITA):c.3012C>T (p.Val1004=) rs751445508 0.00001
NM_000246.4(CIITA):c.3088C>T (p.Leu1030=) rs763766993 0.00001
NM_000246.4(CIITA):c.3149+11C>T rs371453398 0.00001
NM_000246.4(CIITA):c.3233+7G>A rs765558693 0.00001
NM_000246.4(CIITA):c.3264G>A (p.Gly1088=) rs1357870557 0.00001
NM_000246.4(CIITA):c.3317+1G>A rs771073292 0.00001
NM_000246.4(CIITA):c.922C>T (p.Arg308Ter) rs567218474 0.00001
NM_003721.4(RFXANK):c.437G>A (p.Trp146Ter) rs778357787 0.00001
NM_003721.4(RFXANK):c.438+5G>A rs1196984337 0.00001
NM_003721.4(RFXANK):c.454_455del (p.Ile152fs) rs753338285 0.00001
NM_003721.4(RFXANK):c.540C>T (p.Asp180=) rs576657199 0.00001
NM_000246.4(CIITA):c.1044G>T (p.Thr348=) rs140683241
NM_000246.4(CIITA):c.1176G>A (p.Leu392=) rs761978819
NM_000246.4(CIITA):c.1356C>A (p.Pro452=) rs1208913607
NM_000246.4(CIITA):c.1383dup (p.Ala462fs) rs2039198631
NM_000246.4(CIITA):c.1615C>T (p.Arg539Ter) rs751733167
NM_000246.4(CIITA):c.1962del (p.Ala656fs) rs778982759
NM_000246.4(CIITA):c.1962dup (p.Gly655fs) rs778982759
NM_000246.4(CIITA):c.2148C>T (p.Phe716=) rs762483007
NM_000246.4(CIITA):c.2160G>T (p.Leu720=)
NM_000246.4(CIITA):c.2179G>C (p.Glu727Gln) rs548646642
NM_000246.4(CIITA):c.2253G>A (p.Leu751=) rs2544492671
NM_000246.4(CIITA):c.2259C>T (p.Gly753=) rs754313400
NM_000246.4(CIITA):c.2290del (p.Gln764fs) rs1064794659
NM_000246.4(CIITA):c.2317C>T (p.Leu773=) rs767189945
NM_000246.4(CIITA):c.2331G>A (p.Ser777=) rs34685848
NM_000246.4(CIITA):c.2658-10C>T rs1337213724
NM_000246.4(CIITA):c.2816+14C>T rs191941806
NM_000246.4(CIITA):c.2832G>T (p.Ser944=) rs766538754
NM_000246.4(CIITA):c.2889-1G>T rs748505119
NM_000246.4(CIITA):c.3062+14G>A rs370557976
NM_000246.4(CIITA):c.3123G>C (p.Ser1041=) rs138925894
NM_000246.4(CIITA):c.3261C>G (p.Ala1087=) rs149640268
NM_000246.4(CIITA):c.3294G>A (p.Arg1098=) rs1397013056
NM_000246.4(CIITA):c.366A>T (p.Ile122=) rs535705691
NM_000246.4(CIITA):c.414T>C (p.Val138=) rs745772598
NM_000246.4(CIITA):c.436+9del rs1567398077
NM_000246.4(CIITA):c.492C>G (p.Pro164=) rs142478532
NM_000246.4(CIITA):c.531C>T (p.Ser177=) rs188055251
NM_000246.4(CIITA):c.649T>C (p.Leu217=) rs773897183
NM_000246.4(CIITA):c.717G>T (p.Gly239=) rs1596534994
NM_000246.4(CIITA):c.950C>A (p.Ser317Tyr) rs116253192
NM_000246.4(CIITA):c.965C>T (p.Pro322Leu) rs74806537
NM_001025603.2(RFX5):c.859-15C>T rs377295214
NM_003721.4(RFXANK):c.271+1G>C rs759667201
NM_003721.4(RFXANK):c.362A>T (p.Asp121Val) rs104894709
NM_003721.4(RFXANK):c.481del (p.Leu161fs) rs2146492780
NM_003721.4(RFXANK):c.535C>T (p.Arg179Cys) rs115964828
NM_003721.4(RFXANK):c.713-1G>A rs2060720733

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