ClinVar Miner

Submissions for variant NM_001371279.1(REEP1):c.486C>T (p.Asp162=)

gnomAD frequency: 0.00425  dbSNP: rs139806812
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000203687 SCV000259271 benign Hereditary spastic paraplegia 31 2024-01-29 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000203687 SCV000432412 benign Hereditary spastic paraplegia 31 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 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.
GeneDx RCV001705164 SCV000514386 benign not provided 2019-08-22 criteria provided, single submitter clinical testing
Genome Diagnostics Laboratory, The Hospital for Sick Children RCV001847919 SCV002104923 likely benign Hereditary spastic paraplegia 2019-06-01 criteria provided, single submitter clinical testing
Ambry Genetics RCV002336549 SCV002639504 likely benign Inborn genetic diseases 2019-07-11 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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