ClinVar Miner

Submissions for variant NM_000277.3(PAH):c.60+9C>T

gnomAD frequency: 0.00009  dbSNP: rs369454152
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen PAH Variant Curation Expert Panel RCV001279869 SCV004015322 uncertain significance Phenylketonuria 2023-07-23 reviewed by expert panel curation The NM_000277.3:c.60+9C>T variant in PAH is an intronic variant affecting a nucleotide in intron 1. To our knowledge, this variant has not been reported in the literature and results of functional studies are unavailable. The highest population minor allele frequency in gnomAD v2.1.1 is 0.0002803 (7/24972 alleles) in the African/African American population (none of the population data codes are met). The computational splicing predictor SpliceAI gives a score of 0.01 for donor loss suggesting that the variant has no impact on splicing (BP4). There is a ClinVar entry for this variant (Variation ID: 991626, 1 star review status) with one submitter classifying the variant as a variant of uncertain significance and one submitter classifying the variant as likely benign. In summary, this variant meets the criteria to be classified as a variant of uncertain significance for PAH deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen PAH Variant Curation Expert Panel (Specifications Version 2.0): BP4.
Labcorp Genetics (formerly Invitae), Labcorp RCV001279869 SCV001676517 likely benign Phenylketonuria 2023-12-20 criteria provided, single submitter clinical testing
Natera, Inc. RCV001279869 SCV001467003 uncertain significance Phenylketonuria 2020-04-17 no assertion criteria provided clinical testing

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