ClinVar Miner

Submissions for variant NM_006772.3(SYNGAP1):c.1913+5G>A

dbSNP: rs1761021575
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001300295 SCV001489432 pathogenic Intellectual disability, autosomal dominant 5 2022-06-09 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. ClinVar contains an entry for this variant (Variation ID: 1003706). This variant has been observed in individual(s) with clinical features of SYNGAP1-related conditions (Invitae). In at least one individual the variant was observed to be de novo. This variant is not present in population databases (gnomAD no frequency). This sequence change falls in intron 11 of the SYNGAP1 gene. It does not directly change the encoded amino acid sequence of the SYNGAP1 protein. It affects a nucleotide within the consensus splice site.
New York Genome Center RCV001300295 SCV002506891 uncertain significance Intellectual disability, autosomal dominant 5 2021-07-08 criteria provided, single submitter clinical testing The heterozygous c.1913+5G>A splice-region variant identified in intron 11 (of 18) of the SYNGAP1 gene has not been reported in affected individuals in the literature. The variant is absent from the gnomAD(v3) database suggesting it is not a common benign variant in the populations represented in that database. The variant affects an evolutionarily conserved nucleotide and is predicted by multiple in silico tools to alter the wild-type mRNA splicing (TRAP score = 0.97, SPLICING ADAscore = 0.99). Based on the available evidence, the heterozygous c.1913+5G>A splice-region variant identified in the SYNGAP1 gene is reported as a variant of uncertain significance.

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