ClinVar Miner

Submissions for variant NM_001130438.3(SPTAN1):c.1806+4A>G

gnomAD frequency: 0.00005  dbSNP: rs770046688
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000726972 SCV000243075 likely benign not provided 2020-07-31 criteria provided, single submitter clinical testing
Invitae RCV001081620 SCV000562971 likely benign Early infantile epileptic encephalopathy with suppression bursts 2024-01-14 criteria provided, single submitter clinical testing
Eurofins Ntd Llc (ga) RCV000726972 SCV000704582 uncertain significance not provided 2017-01-09 criteria provided, single submitter clinical testing
New York Genome Center RCV001781557 SCV002025598 uncertain significance Developmental and epileptic encephalopathy, 5 2020-04-26 criteria provided, single submitter clinical testing The inherited c.1806+4A>G splice-region variant is located in intron14 (of 56) of the SPTAN1 gene and is predicted by multiple In Silico tools to alter normal mRNA splicing. This variant has not been reported in the affected individuals in the literature. The variant has been reported in ClinVar (Variation ID: 207265). The variant has 0.0002315 allele frequency in the gnomAD database across all populations (58 out of 250,568 heterozygous alleles) and 0.00159 allele frequency in Latino subpopulation represented in gnomAD (55 out of 34,578 heterozygous alleles). The c.1806+4A>G variant affects a moderately conserved nucleotide. Functional studies are required to evaluate the potential pathogenicity of this variant. Based on the available evidence, the inherited c.1806+4A>G splice-region variant in the SPTAN1 gene is assessed as a variant of uncertain significance.
Genome-Nilou Lab RCV001781557 SCV002056538 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 RCV001781557 SCV002495975 uncertain significance Developmental and epileptic encephalopathy, 5 2021-08-31 criteria provided, single submitter clinical testing SPTAN1 NM_001130438.2 intron 14 c.1806+4A>G: This variant has not been reported in the literature but is present in 0.2% (55/34578) of Latino alleles in the Genome Aggregation Database (https://gnomad.broadinstitute.org/variant/9-131345132-A-G?dataset=gnomad_r2_1). This variant is present in ClinVar (Variation ID:207265). Evolutionary conservation and computational predictive tools for this variant are limited or unavailable. This variant is an intronic variant with no predicted change in the amino acid sequence but may have an unknown effect on splicing. Splice prediction tools suggest that this variant may alter splicing. However, further studies are needed to understand its impact. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.

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