Total submissions: 5
| Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
|---|---|---|---|---|---|---|---|---|
| Prevention |
RCV000253910 | SCV000311644 | benign | not specified | criteria provided, single submitter | clinical testing | ||
| Illumina Laboratory Services, |
RCV000017698 | SCV000351247 | benign | Trimethylaminuria | 2018-03-06 | 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 and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. |
| Women's Health and Genetics/Laboratory Corporation of America, |
RCV000253910 | SCV003844445 | benign | not specified | 2023-02-08 | criteria provided, single submitter | clinical testing | Variant summary: FMO3 c.769G>A (p.Val257Met) results in a conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.082 in 251052 control chromosomes in the gnomAD database, including 1103 homozygotes. The observed variant frequency is approximately 14.59 fold of the estimated maximal expected allele frequency for a pathogenic variant in FMO3 causing Trimethylaminuria phenotype (0.0056), which is stand-alone evidence that the variant is benign. At least one publication reports experimental evidence evaluating an impact on protein function. These results showed the variant had no effect on enzyme activity (Stormer_2000). Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. One laboratory classified the variant as pathogenic (OMIM), and one laboratory classified the variant as benign. Based on the evidence outlined above, the variant was classified as benign. |
| Invitae | RCV003669101 | SCV004392226 | benign | not provided | 2024-02-01 | criteria provided, single submitter | clinical testing | |
| OMIM | RCV000017698 | SCV000037975 | pathogenic | Trimethylaminuria | 2017-03-26 | no assertion criteria provided | literature only |