ClinVar Miner

Submissions for variant NM_014140.3(SMARCAL1):c.1271A>T (p.Asp424Val) (rs2066520)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000397091 SCV000334960 likely benign not specified 2015-09-21 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000262629 SCV000427348 likely benign Schimke immuno-osseous dysplasia 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Invitae RCV000262629 SCV000636839 benign Schimke immuno-osseous dysplasia 2020-12-08 criteria provided, single submitter clinical testing
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago RCV000262629 SCV001468393 uncertain significance Schimke immuno-osseous dysplasia 2020-10-01 criteria provided, single submitter clinical testing SMARCAL1 NM_014140.3 exon 7 p.Asp424Val (c.1271A>T):This variant has not been reported in the literature but is present in 0.3% (453/129196) of European alleles, including 2 homozygotes in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/2-217293442-A-T?dataset=gnomad_r2_1). This variant is present in ClinVar, with several labs classifying this variant as Likely Benign or Benign (Variation ID:283080). Evolutionary conservation suggests that this variant may impact the protein; computational predictive tools for this variant are unclear. In summary, data on this variant suggests that this variant does not cause disease, but requires further evidence. Therefore, the clinical significance of this variant is uncertain.
Natera, Inc. RCV000262629 SCV001458571 benign Schimke immuno-osseous dysplasia 2019-12-31 no assertion criteria provided clinical testing
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) RCV001573671 SCV001799898 likely benign not provided no assertion criteria provided clinical testing

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