ClinVar Miner

Submissions for variant NM_001134407.3(GRIN2A):c.415-89902G>A

dbSNP: rs2141916983
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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 RCV001837345 SCV002097893 uncertain significance Landau-Kleffner syndrome 2021-02-09 criteria provided, single submitter clinical testing The deep intronic inherited c.415-89902G>A variant identified in the GRIN2A gene substitutes a moderately conserved Guanine for Adenine (Cytosine for Thymine at the DNA level) within intron 3/13. This variant is absent from gnomAD(v3.1) suggesting it is not a common benign variant in the populations represented in that database. In silico algorithms do not agree on the effect of this variant, as SpliceAI suggest no alteration to splicing, while the Transcript inferred Pathogenicity Score (TraP score) is 0.19, which is >90% score-percentile, suggesting this variant is possibly damaging to splicing. This variant is absent from ClinVar and to our current knowledge has not been reported in affected individuals in the literature. Given the lack of compelling evidence for its pathogenicity, the inherited c.415-89902G>A variant identified in the GRIN2A gene is reported as a Variant of Uncertain Significance

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