The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
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Variant: NM_000232.5(SGCB):c.799C>T (p.Arg267Cys)

CA2918272

283043 (ClinVar)

Gene: SGCB
Condition: autosomal recessive limb-girdle muscular dystrophy
Inheritance Mode: Autosomal recessive inheritance
UUID: afb4eee2-316b-4a50-8626-4d9c20c087d2
Approved on: 2025-01-09
Published on: 2025-01-09

HGVS expressions

NM_000232.5:c.799C>T
NM_000232.5(SGCB):c.799C>T (p.Arg267Cys)
NC_000004.12:g.52024115G>A
CM000666.2:g.52024115G>A
NC_000004.11:g.52890281G>A
CM000666.1:g.52890281G>A
NC_000004.10:g.52585038G>A
NG_008891.1:g.19205C>T
NG_053164.1:g.1197C>T
ENST00000381431.10:c.799C>T
ENST00000381431.9:c.799C>T
NM_000232.4:c.799C>T
More

Benign

Met criteria codes 2
BA1 PP3

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Limb Girdle Muscular Dystrophy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for SGCB Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Limb Girdle Muscular Dystrophy VCEP
The NM_000232.5: c.799C>T variant in SGCB is a missense variant predicted to cause substitution of arginine by cysteine at amino acid 267 (p.Arg267Cys). The filtering allele frequency of this variant is 0.01396 in the South Asian population in gnomAD v2.1.1 (the lower threshold of the 95% CI of 462/30614 exome chromosomes), which is higher than the LGMD VCEP threshold (>0.002) for BA1 and therefore meets this criterion (BA1). The computational predictor REVEL gives a score of 0.75, which exceeds the threshold of ≥0.70, evidence that correlates with impact to DYSF function (PP3). In summary, this variant meets the criteria to be classified as Benign for autosomal recessive limb girdle muscular dystrophy. Although there are both pathogenic and benign types of evidence for this variant, the predictive pathogenic evidence is not considered inconsistent with the final classification. ACMG/AMP criteria applied, as specified by the ClinGen LGMD VCEP (LGMD VCEP specifications version 1.0.0; 01/09/2025): BA1, PP3.
Met criteria codes
BA1
The filtering allele frequency of this variant is 0.01396 in the South Asian population in gnomAD v2.1.1 (the lower threshold of the 95% CI of 462/30614 exome chromosomes), which is higher than the LGMD VCEP threshold (>0.002) for BA1 and therefore meets this criterion (BA1).
PP3
The computational predictor REVEL gives a score of 0.75, which exceeds the threshold of ≥0.70, evidence that correlates with impact to DYSF function (PP3).
Curation History
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