ClinVar Miner

Submissions for variant NM_017739.4(POMGNT1):c.120+3A>G

gnomAD frequency: 0.00019  dbSNP: rs543271070
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000395118 SCV000338873 uncertain significance not provided 2016-01-19 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001231293 SCV001403810 uncertain significance Autosomal recessive limb-girdle muscular dystrophy type 2O; Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3 2024-01-19 criteria provided, single submitter clinical testing This sequence change falls in intron 2 of the POMGNT1 gene. It does not directly change the encoded amino acid sequence of the POMGNT1 protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (rs543271070, gnomAD 0.06%). This variant has not been reported in the literature in individuals affected with POMGNT1-related conditions. ClinVar contains an entry for this variant (Variation ID: 285722). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
GeneDx RCV000395118 SCV001823182 uncertain significance not provided 2022-01-07 criteria provided, single submitter clinical testing Has not been previously published as pathogenic or benign to our knowledge; In silico analysis, which includes splice predictors and evolutionary conservation, suggests this variant may impact gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV004701379 SCV005205077 uncertain significance not specified 2024-06-06 criteria provided, single submitter clinical testing
Natera, Inc. RCV001833353 SCV002090244 uncertain significance Muscle eye brain disease 2019-10-28 no assertion criteria provided clinical testing

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