ClinVar Miner

Submissions for variant NM_001040142.2(SCN2A):c.970+6A>T

gnomAD frequency: 0.00001  dbSNP: rs371629371
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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
New York Genome Center RCV001837307 SCV002097845 uncertain significance Seizures, benign familial infantile, 3; Developmental and epileptic encephalopathy, 11 2021-02-05 criteria provided, single submitter clinical testing The inherited heterozygous c.970+6A>T splice region variantidentified in intron 7 (of 26) of the SCN2A gene has been reported once in gnomAD(v3) database (1 out of 152,148 heterozygous alleles, no homozygotes) indicating it is a rare allele in the populations represented in gnomAD(v3). The affected nucleotide is moderately conserved. The Transcript inferred Pathogenicity Score (TraP) for this variant is 0.749, which is>99% score-percentile suggesting it is probably damaging to the function of the canonical transcript, however SpliceAI does not predict an alteration to splicing. This variant is absent from ClinVar and to our current knowledge has not been reported in affected individualsin the literature. Given the lack of compelling evidence for its pathogenicity, the inherited heterozygous c.970+6A>T splice region variant identified in the SCN2A gene is reported as a Variant of Uncertain Significance.

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