ClinVar Miner

Submissions for variant NM_006946.4(SPTBN2):c.5696G>A (p.Arg1899His)

gnomAD frequency: 0.00004  dbSNP: rs201017398
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV002101121 SCV002395277 likely benign not provided 2022-02-05 criteria provided, single submitter clinical testing
Ambry Genetics RCV003015291 SCV003750473 uncertain significance Inborn genetic diseases 2021-06-18 criteria provided, single submitter clinical testing The c.5696G>A (p.R1899H) alteration is located in exon 27 (coding exon 26) of the SPTBN2 gene. This alteration results from a G to A substitution at nucleotide position 5696, causing the arginine (R) at amino acid position 1899 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV004770404 SCV005380345 uncertain significance not specified 2024-08-22 criteria provided, single submitter clinical testing Variant summary: SPTBN2 c.5696G>A (p.Arg1899His) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 5.6e-05 in 250344 control chromosomes, predominantly at a frequency of 9.8e-05 within the Non-Finnish European subpopulation in the gnomAD database. This frequency is not significantly higher than estimated for a pathogenic variant in SPTBN2 causing Spinocerebellar Ataxia 5, allowing no conclusion about variant significance. To our knowledge, no occurrence of c.5696G>A in individuals affected with Spinocerebellar Ataxia 5 and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 1589623). Based on the evidence outlined above, the variant was classified as uncertain significance.

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