ClinVar Miner

Submissions for variant NM_015046.7(SETX):c.4828C>T (p.Leu1610Phe)

gnomAD frequency: 0.00004  dbSNP: rs749891883
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000696941 SCV000825525 benign Amyotrophic lateral sclerosis type 4; Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2 2024-09-26 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV000696941 SCV000895958 uncertain significance Amyotrophic lateral sclerosis type 4; Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2 2018-10-31 criteria provided, single submitter clinical testing
Ambry Genetics RCV002334326 SCV002638021 uncertain significance Inborn genetic diseases 2024-05-02 criteria provided, single submitter clinical testing The c.4828C>T (p.L1610F) alteration is located in exon 10 (coding exon 8) of the SETX gene. This alteration results from a C to T substitution at nucleotide position 4828, causing the leucine (L) at amino acid position 1610 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Athena Diagnostics RCV002473117 SCV002771066 uncertain significance not provided 2022-06-27 criteria provided, single submitter clinical testing
Breakthrough Genomics, Breakthrough Genomics RCV002473117 SCV005190539 uncertain significance not provided criteria provided, single submitter not provided
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV005240484 SCV005884881 uncertain significance not specified 2024-12-23 criteria provided, single submitter clinical testing Variant summary: SETX c.4828C>T (p.Leu1610Phe) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 4.8e-05 in 251418 control chromosomes, predominantly at a frequency of 0.00011 within the Non-Finnish European subpopulation in the gnomAD database. This frequency is not significantly higher than estimated for a pathogenic variant in SETX causing Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2 (4.8e-05 vs 0.0012), allowing no conclusion about variant significance. To our knowledge, no occurrence of c.4828C>T in individuals affected with Spinocerebellar ataxia, autosomal recessive, with axonal neuropathy 2 and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 574888). Based on the evidence outlined above, the variant was classified as uncertain significance.

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