ClinVar Miner

Submissions for variant NM_000195.5(HPS1):c.198G>A (p.Ser66=) (rs115265574)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000592415 SCV000709335 uncertain significance not provided 2017-06-14 criteria provided, single submitter clinical testing
Johns Hopkins Genomics, Johns Hopkins University RCV000758238 SCV000886876 uncertain significance Hermansky-Pudlak syndrome 1 2019-01-25 criteria provided, single submitter clinical testing This HPS1 variant (rs115265574) has been identified in large population datasets and the minor allele frequency is neither low enough to consider the variant rare (>0.1%) nor high enough to consider it a population polymorphism (>1%) within the African subpopulation (gnomAD: 84/24958 alleles; 0.34%, no homozygotes). A single submitter in ClinVar classifies this variant as uncertain clinical significance (Variation ID: 502551). This variant has not been reported in the literature, to our knowledge. Bioinformatic analysis predicts that this synonymous variant would not affect normal exon 4 splicing, although this has not been confirmed experimentally to our knowledge. Due to insufficient evidence that this variant is deleterious, the clinical significance of c.198G>A is uncertain at this time.
Invitae RCV000592415 SCV001047014 benign not provided 2020-12-07 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000758238 SCV001265832 uncertain significance Hermansky-Pudlak syndrome 1 2018-01-13 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.
Natera, Inc. RCV001275788 SCV001461341 likely benign Hermansky-Pudlak syndrome 2020-01-13 no assertion criteria provided clinical testing

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