Classification
Category 4
CMH MAF
97 /
14969 samples
(0.648%)
97 het.,
0 hom.
(100%)
97 /
29938 total alleles
(0.324%)
Genes
gene: LYST
synonym(s): CHS, CHS1, LYST, ENSG00000143669
NM_000081.3
[CDS]
Reportable
hgvs_c: NM_000081.3:c.7870C>T
reference AA: R
variant AA: W
reference codon: Cgg
variant codon: Tgg
cDNA pos: 8052
CDS pos: 7870
translation impact: non_synonymous
protein sequence:
NP_000072.2
AA pos: 2624
hgvs_p: NP_000072.2:p.Arg2624Trp
blosum: -3
SIFT: deleterious (0.0)
PolyPhen2: possibly_damaging (0.617)
dbSNP
rs150306354
GMAF = 0.0003994
TOPMED_MAF = 0.00239710754332313
ClinVar
454488
clinvar_significance = Likely_benign
clinvar_disease = Chédiak-Higashi syndrome
Exome Variant Server
EVS
EVS MAF (European American/African American/All) = 0.003721,0.000000,0.002460
ExAC
ExAC
| Ethnicity |
Count / Number |
MAF |
| African |
5 / 10396 |
0.0481% |
| America/Latino |
4 / 11486 |
0.0348% |
| East Asian |
0 / 8634 |
0% |
| Finnish |
37 / 6590 |
0.561% |
| Non-Finnish |
263 / 66626 |
0.395% |
| Other |
6 / 904 |
0.664% |
| South Asian |
21 / 16500 |
0.127% |
| Total MAF |
336 / 121136 |
0.277% |
COSMIC
COSMIC Mutation ID = COSV67715039
COSMIC_FATHMM_PREDICTION = PATHOGENIC
COSMIC_MUTATION_SOMATIC_STATUS = true
gnomAD
gnomAD
Source: Genome / Exome
| Ethnicity |
Count / Number |
MAF |
| African |
14 / 24964 |
0.0561% |
| America/Latino |
15 / 35382 |
0.0424% |
| Ashkenazi Jewish |
5 / 10370 |
0.0482% |
| East Asian |
0 / 19940 |
0% |
| Finnish |
142 / 25120 |
0.565% |
| Non-Finnish |
538 / 129102 |
0.417% |
| Other |
26 / 7220 |
0.36% |
| South Asian |
55 / 30610 |
0.18% |
| Korean |
0 / 3804 |
0% |
| Japanese |
0 / 152 |
0% |
| Other East Asian |
0 / 14424 |
0% |
| Bulgarian |
21 / 2668 |
0.787% |
| Estonian |
37 / 4828 |
0.766% |
| North-Western European |
199 / 50786 |
0.392% |
| Southern European |
19 / 11604 |
0.164% |
| Swedish |
127 / 26110 |
0.486% |
| Other non-Finnish European |
135 / 33106 |
0.408% |
| Total MAF |
795 / 282708 |
0.281% |
Export Variant