Total submissions: 5
| Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
|---|---|---|---|---|---|---|---|---|
| Illumina Laboratory Services, |
RCV001096501 | SCV001252718 | uncertain significance | Chédiak-Higashi syndrome | 2018-01-12 | criteria provided, single submitter | clinical testing | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. |
| Invitae | RCV001096501 | SCV001708951 | likely benign | Chédiak-Higashi syndrome | 2024-01-30 | criteria provided, single submitter | clinical testing | |
| Ce |
RCV001532579 | SCV001748201 | likely benign | not provided | 2021-03-01 | criteria provided, single submitter | clinical testing | |
| Genome Diagnostics Laboratory, |
RCV002264180 | SCV002543650 | uncertain significance | Autoinflammatory syndrome | 2018-09-01 | criteria provided, single submitter | clinical testing | |
| Women's Health and Genetics/Laboratory Corporation of America, |
RCV003987782 | SCV004804306 | likely benign | not specified | 2024-01-09 | criteria provided, single submitter | clinical testing | Variant summary: LYST c.6487G>A (p.Ala2163Thr) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00054 in 251256 control chromosomes, predominantly at a frequency of 0.0028 within the South Asian subpopulation in the gnomAD database. The observed variant frequency within South Asian control individuals in the gnomAD database is approximately 2.5 fold of the estimated maximal expected allele frequency for a pathogenic variant in LYST causing Chediak-Higashi Syndrome phenotype (0.0011), strongly suggesting that the variant is a benign polymorphism found primarily in populations of South Asian origin. To our knowledge, no occurrence of c.6487G>A in individuals affected with Chediak-Higashi Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 873939). Based on the evidence outlined above, the variant was classified as likely benign. |