Classification
Category 4
curation
CMH MAF
35 /
14969 samples
(0.234%)
31 het.,
4 hom.
(88.6%)
39 /
29938 total alleles
(0.13%)
Genes
gene: LYST
synonym(s): CHS, CHS1, LYST, ENSG00000143669
NM_000081.3
[CDS]
Reportable
hgvs_c: NM_000081.3:c.368A>G
reference AA: H
variant AA: R
reference codon: cAt
variant codon: cGt
cDNA pos: 550
CDS pos: 368
translation impact: non_synonymous
protein sequence:
NP_000072.2
AA pos: 123
hgvs_p: NP_000072.2:p.His123Arg
blosum: 0
SIFT: tolerated_low_confidence (0.58)
PolyPhen2: benign (0.024)
dbSNP
rs3768067
GMAF = 0.002196
TOPMED_MAF = 0.00093972986748216
ClinVar
296434
clinvar_significance = Conflicting_interpretations_of_pathogenicity
clinvar_disease = Chédiak-Higashi syndrome
ExAC
ExAC
| Ethnicity |
Count / Number |
MAF |
| African |
1 / 10266 |
0.00974% |
| America/Latino |
0 / 11524 |
0% |
| East Asian |
82 / 8618 |
0.951% |
| Finnish |
0 / 6610 |
0% |
| Non-Finnish |
1 / 66540 |
0.0015% |
| Other |
1 / 906 |
0.11% |
| South Asian |
1 / 16492 |
0.00606% |
| Total MAF |
86 / 120956 |
0.0711% |
COSMIC
COSMIC Mutation ID = COSV67704683
COSMIC_FATHMM_PREDICTION = NEUTRAL
COSMIC_MUTATION_SOMATIC_STATUS = true
gnomAD
gnomAD
Source: Genome / Exome
| Ethnicity |
Count / Number |
MAF |
| African |
1 / 24874 |
0.00402% |
| America/Latino |
0 / 34270 |
0% |
| Ashkenazi Jewish |
0 / 10102 |
0% |
| East Asian |
225 / 19614 |
1.15% |
| Finnish |
0 / 24922 |
0% |
| Non-Finnish |
0 / 127454 |
0% |
| Other |
6 / 7048 |
0.0851% |
| South Asian |
1 / 29330 |
0.00341% |
| Korean |
37 / 3788 |
0.977% |
| Japanese |
0 / 152 |
0% |
| Other East Asian |
172 / 14116 |
1.22% |
| Bulgarian |
0 / 2654 |
0% |
| Estonian |
0 / 4832 |
0% |
| North-Western European |
0 / 49930 |
0% |
| Southern European |
0 / 11450 |
0% |
| Swedish |
0 / 25990 |
0% |
| Other non-Finnish European |
0 / 32598 |
0% |
| Total MAF |
233 / 277614 |
0.0839% |
curated_classification = 4
Export Variant