ClinVar Miner

Submissions for variant NM_001130438.3(SPTAN1):c.3051G>A (p.Pro1017=)

gnomAD frequency: 0.00175  dbSNP: rs140279996
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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000147621 SCV000171835 benign not specified 2013-07-25 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Eurofins Ntd Llc (ga) RCV000147621 SCV000227910 benign not specified 2015-03-13 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001083005 SCV000562962 benign Early infantile epileptic encephalopathy with suppression bursts 2024-01-27 criteria provided, single submitter clinical testing
Ambry Genetics RCV002312942 SCV000847600 benign Inborn genetic diseases 2016-08-19 criteria provided, single submitter clinical testing This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Athena Diagnostics RCV000476592 SCV001145802 benign not provided 2018-11-21 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV001808365 SCV002056652 benign Developmental and epileptic encephalopathy, 5 2021-07-15 criteria provided, single submitter clinical testing
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago RCV001808365 SCV003920507 likely benign Developmental and epileptic encephalopathy, 5 2022-08-18 criteria provided, single submitter clinical testing This variant has not been reported in the literature but is present in the Genome Aggregation Database (Highest reported MAF 0.4% (190/41396) (https://gnomad.broadinstitute.org/variant/9-128591521-G-A?dataset=gnomad_r3). This variant is present in ClinVar, with several labs classifying this variant as Benign (Variation ID:139282). Evolutionary conservation and computational predictive tools for this variant are limited or unavailable. Of note, this variant is a silent variant and does not change the amino acid, reducing the probability that this variant is disease causing. In summary, data on this variant suggests that this variant does not cause disease but requires further evidence. Therefore, this variant is classified as likely benign.
Breakthrough Genomics, Breakthrough Genomics RCV000476592 SCV005322440 benign not provided criteria provided, single submitter not provided
Genetic Services Laboratory, University of Chicago RCV000147621 SCV000195070 likely benign not specified no assertion criteria provided clinical testing

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