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_000023.4(SGCA):c.37+23G>A

CA8643656

254719 (ClinVar)

Gene: SGCA
Condition: autosomal recessive limb-girdle muscular dystrophy
Inheritance Mode: Autosomal recessive inheritance
Link to MONDO
UUID: 50002bc0-3631-497f-ab23-e7dd3410f479
Approved on: 2025-01-07
Published on: 2025-01-07

HGVS expressions

NM_000023.4:c.37+23G>A
NM_000023.4(SGCA):c.37+23G>A
NC_000017.11:g.50166100G>A
CM000679.2:g.50166100G>A
NC_000017.10:g.48243461G>A
CM000679.1:g.48243461G>A
NC_000017.9:g.45598460G>A
NG_008889.1:g.5096G>A
ENST00000504073.2:c.37+23G>A
ENST00000511303.6:n.37+23G>A
ENST00000512526.2:c.37+23G>A
ENST00000682109.1:c.37+23G>A
ENST00000683294.1:c.37+23G>A
ENST00000262018.8:c.37+23G>A
ENST00000262018.7:c.37+23G>A
ENST00000344627.10:c.37+23G>A
ENST00000502555.5:c.37+23G>A
ENST00000511303.5:c.33+23G>A
ENST00000513821.5:c.37+23G>A
ENST00000513942.5:n.103+1784G>A
ENST00000514934.1:c.60G>A
NM_000023.2:c.37+23G>A
NM_001135697.1:c.37+23G>A
NM_000023.3:c.37+23G>A
NM_001135697.2:c.37+23G>A
NR_135553.1:n.93+23G>A
NM_001135697.3:c.37+23G>A
NR_135553.2:n.73+23G>A
More

Benign

Met criteria codes 3
BP7 BP4 BA1
Not Met criteria codes 23
PP4 PP1 PP3 PP2 PM3 PM1 PM5 PM4 PM6 PM2 BS2 BS4 BS3 BS1 BP5 BP2 BP1 BP3 PVS1 PS2 PS4 PS3 PS1

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 SGCA 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_000023.4: c.37+23G>A variant in SGCA is located in intron 1 of 9. The filtering allele frequency of this variant in SGCA is 0.06791 (the lower threshold of the 95% CI of 1625/21638 exome chromosomes) in the European (non-Finnish) population in gnomAD v2.1.1, which is higher than the ClinGen LGMD VCEP threshold (>0.002) for BA1 and therefore meets this criterion (BA1). This variant is not located in a splice region and is not predicted to impact splicing by SpliceAI (BP4, BP7). In summary, this variant meets the criteria to be classified as 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; 01/07/2025): BA1, BP4, BP7.
Met criteria codes
BP7
The c.37+23G>A variant is an intronic variant that is not located in a splice region and is not predicted to impact splicing (BP7).
BP4
The splice site predictor SpliceAI indicated that the variant has no impact on splicing (donor loss score of 0.05), evidence that does not predict a damaging effect on SGCA function, given a BP4 threshold of ≤0.05 (BP4).
BA1
The filtering allele frequency of the c.37+23G>A variant in SGCA is 0.06791 (the lower threshold of the 95% CI of 1625/21638 exome chromosomes) in the European (non-Finnish) population in gnomAD v2.1.1, which is higher than the ClinGen LGMD VCEP threshold (>0.002) for BA1 and therefore meets this criterion (BA1).
Not Met criteria codes
PP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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