ClinVar Miner

Submissions for variant NM_145207.3(AFG2A):c.896G>T (p.Gly299Val)

gnomAD frequency: 0.00164  dbSNP: rs75871497
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000536784 SCV000656004 likely benign Microcephaly-intellectual disability-sensorineural hearing loss-epilepsy-abnormal muscle tone syndrome 2025-01-23 criteria provided, single submitter clinical testing
GeneDx RCV001662603 SCV001873666 uncertain significance not provided 2021-06-28 criteria provided, single submitter clinical testing In silico analysis supports a deleterious effect on splicing; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 27535533)
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago RCV000536784 SCV002495972 uncertain significance Microcephaly-intellectual disability-sensorineural hearing loss-epilepsy-abnormal muscle tone syndrome 2022-02-03 criteria provided, single submitter clinical testing SPATA5 NM_145207.2 exon 5 p.Gly299Val (c.896G>T): This variant has not been reported in the literature but is present in 0.5% (230/41448) of African alleles in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/4-122934487-G-T?dataset=gnomad_r3). This variant is present in ClinVar (Variation ID:475737). This variant amino acid Valine (Val) is present in several species including multiple mammals and is not well conserved among evolutionarily distant species; this suggests that this variant may not impact the protein. Additional computational prediction tools do not suggest an impact. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.
PreventionGenetics, part of Exact Sciences RCV003945322 SCV004764442 likely benign AFG2A-related disorder 2020-09-04 no assertion criteria provided clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

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