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:
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
2838 221 0 41 82 0 3 120

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 19 0 0 0
likely pathogenic 19 0 3 0 0
uncertain significance 0 3 0 72 16
likely benign 0 0 72 0 22
benign 0 0 16 22 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 2838 221 0 41 82 0 3 120

All variants with conflicting interpretations #

Total variants: 120
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000081.4(LYST):c.2355T>C (p.Leu785=) rs3768066 0.10928
NM_000081.4(LYST):c.4392C>T (p.Asn1464=) rs11583387 0.09239
NM_000081.4(LYST):c.7137A>C (p.Leu2379=) rs61738992 0.02884
NM_000081.4(LYST):c.9C>T (p.Thr3=) rs33998267 0.01172
NM_000081.4(LYST):c.5945C>T (p.Thr1982Ile) rs146591126 0.00669
NM_000081.4(LYST):c.10941-7C>A rs72761794 0.00614
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 0.00416
NM_000081.4(LYST):c.1686G>C (p.Gln562His) rs77091385 0.00394
NM_000081.4(LYST):c.4863-19T>C rs150288597 0.00393
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.3683A>G (p.Asn1228Ser) rs145553827 0.00171
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 0.00126
NM_000081.4(LYST):c.4548C>T (p.Ser1516=) rs116551057 0.00108
NM_000081.4(LYST):c.7506A>G (p.Gln2502=) rs140434436 0.00106
NM_000081.4(LYST):c.2769A>C (p.Ser923=) rs112739986 0.00086
NM_000081.4(LYST):c.8027G>T (p.Ser2676Ile) rs113209379 0.00086
NM_000081.4(LYST):c.8368A>C (p.Lys2790Gln) rs138506576 0.00061
NM_000081.4(LYST):c.2363+10dup rs760632806 0.00058
NM_000081.4(LYST):c.4637C>T (p.Ala1546Val) rs142983846 0.00054
NM_000081.4(LYST):c.11086G>A (p.Val3696Ile) rs147221131 0.00052
NM_000081.4(LYST):c.692A>G (p.Gln231Arg) rs147433918 0.00043
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.2313G>A (p.Gln771=) rs147220685 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.3394-14T>C rs372892911 0.00029
NM_000081.4(LYST):c.368A>G (p.His123Arg) rs3768067 0.00027
NM_000081.4(LYST):c.6487G>A (p.Ala2163Thr) rs201513511 0.00026
NM_000081.4(LYST):c.7368T>C (p.Asn2456=) rs199631995 0.00026
NM_000081.4(LYST):c.4578T>A (p.Asn1526Lys) rs117609949 0.00025
NM_000081.4(LYST):c.2754G>A (p.Glu918=) rs373577384 0.00022
NM_000081.4(LYST):c.3898A>G (p.Ile1300Val) rs199855658 0.00021
NM_000081.4(LYST):c.4006+8G>A rs369153654 0.00021
NM_000081.4(LYST):c.9045-13T>C rs181450025 0.00021
NM_000081.4(LYST):c.10477T>C (p.Phe3493Leu) rs200511787 0.00020
NM_000081.4(LYST):c.2700A>G (p.Leu900=) rs111463684 0.00017
NM_000081.4(LYST):c.6291C>T (p.Ala2097=) rs199857997 0.00016
NM_000081.4(LYST):c.6388G>A (p.Asp2130Asn) rs148371004 0.00014
NM_000081.4(LYST):c.7806A>G (p.Gln2602=) rs372754364 0.00014
NM_000081.4(LYST):c.1494A>G (p.Arg498=) rs201412615 0.00013
NM_000081.4(LYST):c.2150A>G (p.Asn717Ser) rs201255245 0.00013
NM_000081.4(LYST):c.2517T>C (p.Ile839=) rs78172154 0.00012
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.9520G>A (p.Val3174Ile) rs199672291 0.00008
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.10758C>T (p.Cys3586=) rs145136281 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.2724C>T (p.Cys908=) rs201440611 0.00001
NM_000081.4(LYST):c.3310C>T (p.Arg1104Ter) rs80338652 0.00001
NM_000081.4(LYST):c.10127A>G (p.Asn3376Ser) rs80338669
NM_000081.4(LYST):c.10341G>A (p.Glu3447=)
NM_000081.4(LYST):c.10345C>T (p.Arg3449Ter) rs754616030
NM_000081.4(LYST):c.10740G>A (p.Leu3580=)
NM_000081.4(LYST):c.11038+11T>C
NM_000081.4(LYST):c.11076C>T (p.Asn3692=)
NM_000081.4(LYST):c.11229A>G (p.Arg3743=)
NM_000081.4(LYST):c.11268-17dup rs36014994
NM_000081.4(LYST):c.11268-5del rs36014994
NM_000081.4(LYST):c.11268-6_11268-5del rs36014994
NM_000081.4(LYST):c.1664A>C (p.His555Pro)
NM_000081.4(LYST):c.1722A>G (p.Leu574=)
NM_000081.4(LYST):c.1725G>A (p.Ser575=)
NM_000081.4(LYST):c.192+1G>A
NM_000081.4(LYST):c.244C>T (p.Leu82=)
NM_000081.4(LYST):c.285T>C (p.Asp95=)
NM_000081.4(LYST):c.2962C>T (p.Arg988Ter)
NM_000081.4(LYST):c.3433del (p.His1145fs)
NM_000081.4(LYST):c.345A>G (p.Gln115=)
NM_000081.4(LYST):c.3601del (p.Ser1201fs)
NM_000081.4(LYST):c.3712+12T>C
NM_000081.4(LYST):c.372A>G (p.Leu124=)
NM_000081.4(LYST):c.3940-17dup
NM_000081.4(LYST):c.3996del (p.Asp1333fs)
NM_000081.4(LYST):c.4053A>G (p.Ser1351=)
NM_000081.4(LYST):c.5023+14G>A
NM_000081.4(LYST):c.5461-14A>T
NM_000081.4(LYST):c.5461-3del rs557545474
NM_000081.4(LYST):c.5491C>T (p.Gln1831Ter)
NM_000081.4(LYST):c.5583T>C (p.Ile1861=)
NM_000081.4(LYST):c.5634+11A>G
NM_000081.4(LYST):c.5674A>G (p.Met1892Val)
NM_000081.4(LYST):c.5719A>G (p.Ile1907Val)
NM_000081.4(LYST):c.6122-13del rs201404906
NM_000081.4(LYST):c.6673C>T (p.Arg2225Cys)
NM_000081.4(LYST):c.6744A>G (p.Leu2248=)
NM_000081.4(LYST):c.6862C>T (p.Arg2288Ter)
NM_000081.4(LYST):c.7135dup (p.Leu2379fs)
NM_000081.4(LYST):c.7460+3_7460+6del
NM_000081.4(LYST):c.8152-8G>A
NM_000081.4(LYST):c.8358+2T>C
NM_000081.4(LYST):c.8425dup (p.Glu2809fs)
NM_000081.4(LYST):c.8742A>G (p.Lys2914=)
NM_000081.4(LYST):c.8802-2A>G
NM_000081.4(LYST):c.8869C>T (p.Arg2957Ter)
NM_000081.4(LYST):c.9162+11G>A
NM_000081.4(LYST):c.9162+15A>G
NM_000081.4(LYST):c.9219_9222del (p.Glu3074fs)
NM_000081.4(LYST):c.9244T>C (p.Leu3082=)
NM_000081.4(LYST):c.9245dup (p.Leu3082fs)
NM_000081.4(LYST):c.985C>T (p.Arg329Ter)
NM_000081.4(LYST):c.9874G>T (p.Glu3292Ter)
NM_000081.4(LYST):c.9969C>T (p.His3323=)
NM_000081.4(LYST):c.9988del (p.Ala3330fs)
NM_000081.4(LYST):c.9990G>A (p.Ala3330=)

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