ClinVar Miner

Submissions for variant NM_000232.5(SGCB):c.519G>A (p.Pro173=)

gnomAD frequency: 0.00005  dbSNP: rs755701680
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Limb Girdle Muscular Dystrophy Variant Curation Expert Panel, ClinGen RCV004997503 SCV005620291 likely benign Autosomal recessive limb-girdle muscular dystrophy 2025-01-09 reviewed by expert panel curation The NM_000232.5: c.519G>A p.(Pro173=) variant in SGCB is a synonymous (silent) variant that is not predicted to influence splicing by SpliceAI (score 0.03) (BP4, BP7). The filtering allele frequency of the variant is 0.0005025 for East Asian genome chromosomes in gnomAD v3.1.2 (the lower threshold of the 95% CI of 6/5192), which is lower than the VCEP threshold of 0.001 (BS1 not met; PM2_Supporting also not met). In summary, this variant meets the criteria to be classified as Likely Benign for autosomal recessive limb girdle muscular dystrophy based on the ACMG/AMP criteria applied, as specified by the ClinGen LGMD VCEP (LGMD VCEP specifications version 1.0.0; 01/09/2025): BP4, BP7.
Labcorp Genetics (formerly Invitae), Labcorp RCV000923149 SCV001068612 likely benign Autosomal recessive limb-girdle muscular dystrophy type 2E 2024-06-24 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV001148507 SCV001309406 uncertain significance Qualitative or quantitative defects of beta-sarcoglycan 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.

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