ClinVar Miner

Variants with conflicting interpretations studied for Chédiak-Higashi syndrome

Coded as:
Minimum review status of the submission for Chédiak-Higashi syndrome: Collection method of the submission for Chédiak-Higashi syndrome:
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
3249 240 0 48 74 0 3 122

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
Chédiak-Higashi syndrome pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 31 0 0 0
likely pathogenic 31 0 3 0 0
uncertain significance 0 3 0 66 11
likely benign 0 0 66 0 17
benign 0 0 11 17 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
Chédiak-Higashi syndrome 3249 240 0 48 74 0 3 122

All variants with conflicting interpretations #

Total variants: 122
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000081.4(LYST):c.5945C>T (p.Thr1982Ile) rs146591126 0.00646
NM_000081.4(LYST):c.10941-7C>A rs72761794 0.00629
NM_000081.4(LYST):c.5518T>G (p.Ser1840Ala) rs115330112 0.00485
NM_000081.4(LYST):c.10800+4G>T rs41308172 0.00441
NM_000081.4(LYST):c.6482A>C (p.Glu2161Ala) rs147756847 0.00421
NM_000081.4(LYST):c.1686G>C (p.Gln562His) rs77091385 0.00380
NM_000081.4(LYST):c.4863-19T>C rs150288597 0.00373
NM_000081.4(LYST):c.6292G>A (p.Ala2098Thr) rs146091043 0.00315
NM_000081.4(LYST):c.7870C>T (p.Arg2624Trp) rs150306354 0.00280
NM_000081.4(LYST):c.8913T>G (p.Asn2971Lys) rs34702903 0.00276
NM_000081.4(LYST):c.2363+4T>C rs201398337 0.00252
NM_000081.4(LYST):c.5023+14G>A rs115581194 0.00234
NM_000081.4(LYST):c.3683A>G (p.Asn1228Ser) rs145553827 0.00157
NM_000081.4(LYST):c.6710A>C (p.Gln2237Pro) rs138443479 0.00148
NM_000081.4(LYST):c.4337G>A (p.Arg1446Gln) rs111722949 0.00135
NM_000081.4(LYST):c.8487C>T (p.Ile2829=) rs144597913 0.00125
NM_000081.4(LYST):c.4548C>T (p.Ser1516=) rs116551057 0.00108
NM_000081.4(LYST):c.2769A>C (p.Ser923=) rs112739986 0.00086
NM_000081.4(LYST):c.8027G>T (p.Ser2676Ile) rs113209379 0.00083
NM_000081.4(LYST):c.4637C>T (p.Ala1546Val) rs142983846 0.00080
NM_000081.4(LYST):c.11086G>A (p.Val3696Ile) rs147221131 0.00055
NM_000081.4(LYST):c.8368A>C (p.Lys2790Gln) rs138506576 0.00044
NM_000081.4(LYST):c.692A>G (p.Gln231Arg) rs147433918 0.00042
NM_000081.4(LYST):c.6487G>A (p.Ala2163Thr) rs201513511 0.00040
NM_000081.4(LYST):c.1655T>C (p.Val552Ala) rs199617821 0.00038
NM_000081.4(LYST):c.2946T>C (p.Tyr982=) rs145892183 0.00034
NM_000081.4(LYST):c.368A>G (p.His123Arg) rs3768067 0.00032
NM_000081.4(LYST):c.2150A>G (p.Asn717Ser) rs201255245 0.00031
NM_000081.4(LYST):c.2313G>A (p.Gln771=) rs147220685 0.00031
NM_000081.4(LYST):c.5634+11A>G rs373971587 0.00031
NM_000081.4(LYST):c.6782G>A (p.Arg2261His) rs147791378 0.00031
NM_000081.4(LYST):c.2963G>A (p.Arg988Gln) rs150953050 0.00029
NM_000081.4(LYST):c.4578T>A (p.Asn1526Lys) rs117609949 0.00025
NM_000081.4(LYST):c.9045-13T>C rs181450025 0.00025
NM_000081.4(LYST):c.2754G>A (p.Glu918=) rs373577384 0.00023
NM_000081.4(LYST):c.4006+8G>A rs369153654 0.00021
NM_000081.4(LYST):c.3898A>G (p.Ile1300Val) rs199855658 0.00019
NM_000081.4(LYST):c.6291C>T (p.Ala2097=) rs199857997 0.00016
NM_000081.4(LYST):c.10477T>C (p.Phe3493Leu) rs200511787 0.00014
NM_000081.4(LYST):c.6388G>A (p.Asp2130Asn) rs148371004 0.00014
NM_000081.4(LYST):c.1494A>G (p.Arg498=) rs201412615 0.00013
NM_000081.4(LYST):c.3712+12T>C rs374949148 0.00013
NM_000081.4(LYST):c.7806A>G (p.Gln2602=) rs372754364 0.00013
NM_000081.4(LYST):c.1664A>C (p.His555Pro) rs201106245 0.00012
NM_000081.4(LYST):c.1722A>G (p.Leu574=) rs762078094 0.00011
NM_000081.4(LYST):c.2517T>C (p.Ile839=) rs78172154 0.00011
NM_000081.4(LYST):c.2700A>G (p.Leu900=) rs111463684 0.00011
NM_000081.4(LYST):c.10221C>T (p.Tyr3407=) rs146457386 0.00010
NM_000081.4(LYST):c.196T>C (p.Leu66=) rs138393416 0.00010
NM_000081.4(LYST):c.2826A>G (p.Pro942=) rs149558986 0.00010
NM_000081.4(LYST):c.281C>T (p.Thr94Ile) rs777389303 0.00009
NM_000081.4(LYST):c.6673C>T (p.Arg2225Cys) rs375665715 0.00009
NM_000081.4(LYST):c.9162+11G>A rs74958355 0.00009
NM_000081.4(LYST):c.9969C>T (p.His3323=) rs200610828 0.00009
NM_000081.4(LYST):c.9520G>A (p.Val3174Ile) rs199672291 0.00008
NM_000081.4(LYST):c.9162+15A>G rs374429343 0.00007
NM_000081.4(LYST):c.3030A>G (p.Gly1010=) rs751511204 0.00006
NM_000081.4(LYST):c.3834G>A (p.Leu1278=) rs148542548 0.00006
NM_000081.4(LYST):c.4983G>A (p.Leu1661=) rs1482156206 0.00006
NM_000081.4(LYST):c.5635-4A>G rs754201076 0.00006
NM_000081.4(LYST):c.7911G>A (p.Thr2637=) rs140229368 0.00006
NM_000081.4(LYST):c.244C>T (p.Leu82=) rs376821187 0.00005
NM_000081.4(LYST):c.5719A>G (p.Ile1907Val) rs370441301 0.00005
NM_000081.4(LYST):c.1725G>A (p.Ser575=) rs144919024 0.00004
NM_000081.4(LYST):c.5461-14A>T rs768616413 0.00004
NM_000081.4(LYST):c.10740G>A (p.Leu3580=) rs773942795 0.00003
NM_000081.4(LYST):c.10758C>T (p.Cys3586=) rs145136281 0.00003
NM_000081.4(LYST):c.11076C>T (p.Asn3692=) rs368394921 0.00003
NM_000081.4(LYST):c.11229A>G (p.Arg3743=) rs368618083 0.00003
NM_000081.4(LYST):c.4566A>C (p.Ala1522=) rs142344106 0.00003
NM_000081.4(LYST):c.4632C>T (p.Ser1544=) rs373930104 0.00003
NM_000081.4(LYST):c.5674A>G (p.Met1892Val) rs200512692 0.00003
NM_000081.4(LYST):c.8152-8G>A rs569497153 0.00002
NM_000081.4(LYST):c.10127A>G (p.Asn3376Ser) rs80338669 0.00001
NM_000081.4(LYST):c.10341G>A (p.Glu3447=) rs752160342 0.00001
NM_000081.4(LYST):c.10883dup (p.Tyr3628Ter) rs1238562877 0.00001
NM_000081.4(LYST):c.11038+11T>C rs1659440744 0.00001
NM_000081.4(LYST):c.2724C>T (p.Cys908=) rs201440611 0.00001
NM_000081.4(LYST):c.3310C>T (p.Arg1104Ter) rs80338652 0.00001
NM_000081.4(LYST):c.372A>G (p.Leu124=) rs1233751084 0.00001
NM_000081.4(LYST):c.4053A>G (p.Ser1351=) rs752123968 0.00001
NM_000081.4(LYST):c.5583T>C (p.Ile1861=) rs979729264 0.00001
NM_000081.4(LYST):c.5956C>T (p.Arg1986Ter) rs1188244229 0.00001
NM_000081.4(LYST):c.7836A>G (p.Ser2612=) rs886046174 0.00001
NM_000081.4(LYST):c.8358+2T>C rs1157079200 0.00001
NM_000081.4(LYST):c.9244T>C (p.Leu3082=) rs906201774 0.00001
NM_000081.4(LYST):c.9838C>T (p.Arg3280Ter) rs201694319 0.00001
NM_000081.4(LYST):c.10066C>T (p.Gln3356Ter)
NM_000081.4(LYST):c.10345C>T (p.Arg3449Ter) rs754616030
NM_000081.4(LYST):c.10643T>A (p.Leu3548Ter) rs2527258082
NM_000081.4(LYST):c.11268-5del rs36014994
NM_000081.4(LYST):c.148C>T (p.Arg50Ter) rs80338643
NM_000081.4(LYST):c.192+1G>A rs2527299680
NM_000081.4(LYST):c.2016C>A (p.Tyr672Ter) rs922968465
NM_000081.4(LYST):c.2413G>T (p.Glu805Ter) rs762160809
NM_000081.4(LYST):c.285T>C (p.Asp95=) rs747965676
NM_000081.4(LYST):c.2962C>T (p.Arg988Ter) rs1236600542
NM_000081.4(LYST):c.3433del (p.His1145fs) rs760317441
NM_000081.4(LYST):c.345A>G (p.Gln115=) rs2527133215
NM_000081.4(LYST):c.3601del (p.Ser1201fs) rs2527037759
NM_000081.4(LYST):c.3940-17dup rs755137786
NM_000081.4(LYST):c.3996del (p.Asp1333fs) rs2527008662
NM_000081.4(LYST):c.4433G>A (p.Trp1478Ter) rs2526908416
NM_000081.4(LYST):c.484C>T (p.Gln162Ter) rs1346059141
NM_000081.4(LYST):c.5461-3del rs557545474
NM_000081.4(LYST):c.5491C>T (p.Gln1831Ter) rs2527973482
NM_000081.4(LYST):c.6712C>T (p.Arg2238Ter) rs2527805640
NM_000081.4(LYST):c.6744A>G (p.Leu2248=) rs886046176
NM_000081.4(LYST):c.6862C>T (p.Arg2288Ter) rs1667309466
NM_000081.4(LYST):c.7135dup (p.Leu2379fs) rs1449954533
NM_000081.4(LYST):c.7460+3_7460+6del rs2527732015
NM_000081.4(LYST):c.8156C>G (p.Ser2719Ter)
NM_000081.4(LYST):c.8425dup (p.Glu2809fs) rs2527559893
NM_000081.4(LYST):c.8742A>G (p.Lys2914=) rs886046172
NM_000081.4(LYST):c.8802-2A>G rs2527531929
NM_000081.4(LYST):c.8869C>T (p.Arg2957Ter) rs1227624153
NM_000081.4(LYST):c.9219_9222del (p.Glu3074fs) rs1394834891
NM_000081.4(LYST):c.9245dup (p.Leu3082fs) rs1663631401
NM_000081.4(LYST):c.985C>T (p.Arg329Ter) rs1673263416
NM_000081.4(LYST):c.9874G>T (p.Glu3292Ter) rs778586545
NM_000081.4(LYST):c.9988del (p.Ala3330fs) rs2527364273
NM_000081.4(LYST):c.9990G>A (p.Ala3330=) rs912444962

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