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
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_001130987.2(DYSF):c.4629C>G (p.Val1543=)

CA245628

197463 (ClinVar)

Gene: DYSF
Condition: autosomal recessive limb-girdle muscular dystrophy
Inheritance Mode: Autosomal recessive inheritance
UUID: 919e209e-3af2-4260-899b-a4a468b01330
Approved on: 2025-01-09
Published on: 2025-01-09

HGVS expressions

NM_001130987.2:c.4629C>G
NM_001130987.2(DYSF):c.4629C>G (p.Val1543=)
NC_000002.12:g.71656164C>G
CM000664.2:g.71656164C>G
NC_000002.11:g.71883294C>G
CM000664.1:g.71883294C>G
NC_000002.10:g.71736802C>G
NG_008694.1:g.207542C>G
ENST00000698057.1:c.2043C>G
ENST00000698058.1:c.1260C>G
ENST00000698059.1:c.1368C>G
ENST00000258104.8:c.4512C>G
ENST00000410020.8:c.4629C>G
ENST00000258104.7:c.4512C>G
ENST00000394120.6:c.4515C>G
ENST00000409366.5:c.4578C>G
ENST00000409582.7:c.4626C>G
ENST00000409651.5:c.4608C>G
ENST00000409744.5:c.4536C>G
ENST00000409762.5:c.4563C>G
ENST00000410020.7:c.4629C>G
ENST00000410041.1:c.4566C>G
ENST00000413539.6:c.4605C>G
ENST00000429174.6:c.4575C>G
ENST00000479049.6:n.1397C>G
NM_001130455.1:c.4515C>G
NM_001130976.1:c.4470C>G
NM_001130977.1:c.4533C>G
NM_001130978.1:c.4575C>G
NM_001130979.1:c.4605C>G
NM_001130980.1:c.4563C>G
NM_001130981.1:c.4626C>G
NM_001130982.1:c.4608C>G
NM_001130983.1:c.4578C>G
NM_001130984.1:c.4536C>G
NM_001130985.1:c.4566C>G
NM_001130986.1:c.4473C>G
NM_001130987.1:c.4629C>G
NM_003494.3:c.4512C>G
NM_001130455.2:c.4515C>G
NM_001130976.2:c.4470C>G
NM_001130977.2:c.4533C>G
NM_001130978.2:c.4575C>G
NM_001130979.2:c.4605C>G
NM_001130980.2:c.4563C>G
NM_001130981.2:c.4626C>G
NM_001130982.2:c.4608C>G
NM_001130983.2:c.4578C>G
NM_001130984.2:c.4536C>G
NM_001130985.2:c.4566C>G
NM_001130986.2:c.4473C>G
NM_003494.4:c.4512C>G
More

Likely Benign

Met criteria codes 2
BS1 BP4
Not Met criteria codes 2
BP5 BP7

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 DYSF 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_003494.4: c.4512C>G p.(Val1504=) variant in DYSF, which is also known as NM_001130987.2: c.4629C>G p.(Val1543=), is a synonymous (silent) variant that is not expected to change the amino acid sequence. The filtering allele frequency for this variant is 0.001985 for the European (non-Finnish) population in gnomAD v4.1.0 (the lower threshold of the 95% CI of 2286/1111986 exome chromosomes), which is greater than the ClinGen LGMD VCEP threshold of 0.001 for BS1, and therefore meets this criterion (BS1). While this variant affects the first amino acid of exon 42 and so is located in a splice region (BP7 not met), the SpliceAI score is 0, which is less than the LGMD VCEP threshold of 0.05 (BP4). This variant has been identified in a patient with a clinical suspicion of LGMD but as a single hit in an individual with an alternative molecular diagnosis (LOVD Individual #00220067). 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): BS1, BP4.
Met criteria codes
BS1
The filtering allele frequency for this variant is 0.001985 for the European (non-Finnish) population in gnomAD v4.1.0 (the lower threshold of the 95% CI of 2286/1111986 exome chromosomes), which is greater than the ClinGen LGMD VCEP threshold of 0.001 for BS1, and therefore meets this criterion (BS1).
BP4
The SpliceAI score for this variant is 0, which is less than the LGMD VCEP threshold of 0.05 (BP4).
Not Met criteria codes
BP5
Identified as a single hit in an individual homozygous for a pathogenic variant in FKRP (LOVD Individual #00220067).
BP7
This variant affects the first amino acid of exon 42 and so is located in a splice region (+7/-21) (BP7 not met).
Curation History
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