ClinVar Miner

Submissions for variant NM_006623.4(PHGDH):c.624T>C (p.Pro208=)

gnomAD frequency: 0.00154  dbSNP: rs77401816
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000358986 SCV000347886 benign PHGDH deficiency 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 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.
Invitae RCV000358986 SCV000766585 benign PHGDH deficiency 2024-01-31 criteria provided, single submitter clinical testing
Athena Diagnostics RCV000712536 SCV000843051 benign not provided 2018-05-15 criteria provided, single submitter clinical testing
GeneDx RCV000712536 SCV001982943 likely benign not provided 2021-04-08 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV003338517 SCV004049080 likely benign Neu-Laxova syndrome 1 2023-04-11 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000358986 SCV004049081 likely benign PHGDH deficiency 2023-04-11 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV003910055 SCV004719242 benign PHGDH-related disorder 2021-06-30 criteria provided, single submitter clinical testing This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
Natera, Inc. RCV000358986 SCV001460688 benign PHGDH deficiency 2020-09-16 no assertion criteria provided clinical testing

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