ClinVar Miner

Submissions for variant NM_000548.5(TSC2):c.1257+5G>A

dbSNP: rs2151157428
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet RCV002226880 SCV002505773 likely pathogenic Tuberous sclerosis 2 2021-08-01 criteria provided, single submitter clinical testing
New York Genome Center RCV002226880 SCV002564272 uncertain significance Tuberous sclerosis 2 2022-02-23 criteria provided, single submitter clinical testing The mosaic c.1257+5G>A variant in TSC2 has not previously been reported in the literature or public variant repositories (ClinVar and LOVD), and is absent from population databases (gnomAD v2.1.1 and v3.1.2, TOPMed Freeze 8), suggesting it is not a common benign variant in the populations represented in those databases. The c.1257+5G>A variant was detected at ~10% mosaicism level (4/39 reads) in this individual. The c.1257+5G>A variant is located in the splice region after exon 12of this 41-exon gene, and is predicted to result in loss of native splice donor site (splice AI donor loss= 0.89) and activate a new splice donor site 12 nucleotides downstream of the variant (splice AI donor gain = 0.61); however, there are no functional studies to support or refute these predictions. Based on available evidence this mosaic heterozygous c.1257+5G>A variant in TSC2 identified is classified as a Variant of Uncertain Significance.

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