Classification
Category 4
curation
CMH MAF
184 /
14969 samples
(1.23%)
183 het.,
1 hom.
(99.5%)
185 /
29938 total alleles
(0.618%)
Genes
gene: LYST
synonym(s): CHS, CHS1, LYST, ENSG00000143669
NM_000081.3
[CDS]
Reportable
hgvs_c: NM_000081.3:c.5518T>G
reference AA: S
variant AA: A
reference codon: Tca
variant codon: Gca
cDNA pos: 5700
CDS pos: 5518
translation impact: non_synonymous
protein sequence:
NP_000072.2
AA pos: 1840
hgvs_p: NP_000072.2:p.Ser1840Ala
blosum: 1
SIFT: tolerated (0.08)
PolyPhen2: benign (0.003)
dbSNP
rs115330112
GMAF = 0.001797
TOPMED_MAF = 0.00482607033639143
ClinVar
235239
clinvar_significance = Conflicting_interpretations_of_pathogenicity
clinvar_disease = Chédiak-Higashi syndrome
Exome Variant Server
EVS
EVS MAF (European American/African American/All) = 0.008264,0.001816,0.006078
ExAC
ExAC
| Ethnicity |
Count / Number |
MAF |
| African |
18 / 10308 |
0.175% |
| America/Latino |
26 / 11406 |
0.228% |
| East Asian |
0 / 8514 |
0% |
| Finnish |
7 / 6554 |
0.107% |
| Non-Finnish |
470 / 66248 |
0.709% |
| Other |
3 / 898 |
0.334% |
| South Asian |
34 / 16462 |
0.207% |
| Total MAF |
558 / 120390 |
0.463% |
gnomAD
gnomAD
Source: Genome / Exome
| Ethnicity |
Count / Number |
MAF |
| African |
39 / 24948 |
0.156% |
| America/Latino |
72 / 35364 |
0.204% |
| Ashkenazi Jewish |
52 / 10360 |
0.502% |
| East Asian |
0 / 19882 |
0% |
| Finnish |
27 / 24740 |
0.109% |
| Non-Finnish |
956 / 128674 |
0.743% |
| Other |
32 / 7186 |
0.445% |
| South Asian |
60 / 30600 |
0.196% |
| Korean |
0 / 3752 |
0% |
| Japanese |
0 / 150 |
0% |
| Other East Asian |
0 / 14422 |
0% |
| Bulgarian |
10 / 2668 |
0.375% |
| Estonian |
8 / 4830 |
0.166% |
| North-Western European |
461 / 50592 |
0.911% |
| Southern European |
36 / 11564 |
0.311% |
| Swedish |
208 / 26070 |
0.798% |
| Other non-Finnish European |
233 / 32950 |
0.707% |
| Total MAF |
1238 / 281754 |
0.439% |
curated_classification = 4
Export Variant