Evidence Repository
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_001100.4(ACTA1):c.617-5C>T

CA1442820

257447 (ClinVar)

Gene: ACTA1
Condition: alpha-actinopathy
Inheritance Mode: Autosomal recessive inheritance
Link to MONDO
UUID: 73f7dd92-b53f-43f3-aeb1-dad2252eb5af
Approved on: 2024-08-07
Published on: 2024-12-19

HGVS expressions

NM_001100.4:c.617-5C>T
NM_001100.4(ACTA1):c.617-5C>T
NC_000001.11:g.229432190G>A
CM000663.2:g.229432190G>A
NC_000001.10:g.229567937G>A
CM000663.1:g.229567937G>A
NC_000001.9:g.227634560G>A
NG_006672.1:g.6907C>T
ENST00000366683.4:c.617-5C>T
ENST00000684723.1:c.482-5C>T
ENST00000366683.3:c.479+217C>T
ENST00000366684.7:c.617-5C>T
NM_001100.3:c.617-5C>T
More

Benign

Met criteria codes 3
BA1 BP4 BP7

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Congenital Myopathies Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for ACTA1 Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Congenital Myopathies VCEP
The NM_001100.4:c.617-5C>T variant in ACTA1 is an intronic variant which is located in the 3’ non-canonical splice site of intron 4. The population filtering allele frequency in gnomAD v4.1.0 is 0.01304 (1030/75010 alleles) in the African/African American population, which is higher than the ClinGen Congenital Myopathies VCEP threshold for BA1, and therefore meets this criterion (BA1). The results from the in silico predictor, SpliceAI, suggest that the variant does not impact ACTA1 function and it occurs at a nucleotide that is not conserved as shown by the UCSC Browser (BP4, BP7). In summary, this variant meets the criteria to be classified as benign for alpha-actinopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen Congenital Myopathies VCEP: BA1, BP4, BP7 (ClinGen Congenital Myopathies VCEP specifications version 1; 08/07/2024).
Met criteria codes
BA1
The population filtering allele frequency in gnomAD v4.1.0 is 0.01304 (1030/75010 alleles) in the African/African American population, which is higher than the ClinGen Congenital Myopathies VCEP threshold for BA1, and therefore meets this criterion (BA1).
BP4
The results from the in silico predictor, SpliceAI, suggest that the variant does not impact ACTA1 function and it occurs at a nucleotide that is not conserved as shown by the UCSC Browser (BP4, BP7).
BP7
The results from the in silico predictor, SpliceAI, suggest that the variant does not impact ACTA1 function and it occurs at a nucleotide that is not conserved as shown by the UCSC Browser (BP4, BP7).
Curation History
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