ClinVar Miner

Submissions for variant NM_014363.6(SACS):c.4466A>G (p.Asn1489Ser)

gnomAD frequency: 0.00597  dbSNP: rs147099630
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Total submissions: 18
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PROSPAX: an integrated multimodal progression chart in spastic ataxias, Center for Neurology; Hertie-Institute for Clinical Brain Research RCV000709972 SCV005061963 likely pathogenic Charlevoix-Saguenay spastic ataxia 2022-01-01 criteria provided, single submitter research
CeGaT Center for Human Genetics Tuebingen RCV001358184 SCV004136811 benign not provided 2025-06-01 criteria provided, single submitter clinical testing SACS: BP4, BS1, BS2
Genome Diagnostics Laboratory, The Hospital for Sick Children RCV001847872 SCV002105043 benign Hereditary spastic paraplegia 2021-04-26 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000193608 SCV002050976 likely benign not specified 2021-12-10 criteria provided, single submitter clinical testing
GeneDx RCV001358184 SCV001906941 benign not provided 2018-10-11 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 26539891, 27980752)
Genome-Nilou Lab RCV000709972 SCV001737291 likely benign Charlevoix-Saguenay spastic ataxia 2021-06-10 criteria provided, single submitter clinical testing
Pars Genome Lab RCV000709972 SCV001652855 likely benign Charlevoix-Saguenay spastic ataxia 2021-05-18 criteria provided, single submitter clinical testing
Athena Diagnostics RCV000193608 SCV001476820 benign not specified 2024-04-15 criteria provided, single submitter clinical testing
Mendelics RCV000709972 SCV001138917 likely benign Charlevoix-Saguenay spastic ataxia 2019-05-28 criteria provided, single submitter clinical testing
Eurofins Ntd Llc (ga) RCV000193608 SCV000704701 benign not specified 2016-12-23 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000475223 SCV000562822 benign Spastic paraplegia 2025-01-27 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV000193608 SCV000248786 benign not specified 2019-08-27 criteria provided, single submitter clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV001358184 SCV001970575 likely benign not provided no assertion criteria provided clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht RCV001358184 SCV001929724 likely benign not provided no assertion criteria provided clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001358184 SCV001553855 benign not provided 2025-06-06 no assertion criteria provided clinical testing The SACS p.Asn1489Ser variant was not identified in the literature. The p.Asn1489Ser variant was identified in dbSNP (ID: rs147099630) and ClinVar (classified as benign 7X by GeneDx, Labcorp Genetics (formerly Invitae), Labcorp and 5 other submitters; likely benign 4X; likely pathogenic 1X). The variant was identified in control databases in 12414 of 1610306 chromosomes (117 homozygous) at a frequency of 0.007709, and was observed at the highest frequency in the Ashkenazi Jewish population in 1260 of 29460 chromosomes (freq: 0.04277) (Genome Aggregation Database April 19, 2024, v4.1.0). The p.Asn1489Ser residue is conserved in mammals and computational analyses (MUT Assesor, PolyPhen-2, SIFT, MutationTaster, Revel, FATHMM, MetaLR, DANN) do not suggest a high likelihood of impact to the protein; this information is not predictive enough to rule out pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (Splice AI exome) do not predict a deleterious effect on splicing. In summary, based on the above information this variant meets our laboratory's criteria to be classified as benign.
Natera, Inc. RCV000709972 SCV001463616 benign Charlevoix-Saguenay spastic ataxia 2020-09-16 no assertion criteria provided clinical testing
GenomeConnect, ClinGen RCV000709972 SCV000840336 not provided Charlevoix-Saguenay spastic ataxia no assertion provided phenotyping only GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.
Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine RCV000454342 SCV000537975 likely pathogenic Abnormal brain morphology flagged submission research

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