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_000231.3(SGCG):c.1-3C>T

CA6909546

805445 (ClinVar)

Gene: SGCG
Condition: autosomal recessive limb-girdle muscular dystrophy
Inheritance Mode: Autosomal recessive inheritance
Link to MONDO
UUID: 5027e7d8-3dd1-4e95-b743-ba88c7fc223f
Approved on: 2025-01-08
Published on: 2025-01-08

HGVS expressions

NM_000231.3:c.1-3C>T
NM_000231.3(SGCG):c.1-3C>T
NC_000013.11:g.23203692C>T
CM000675.2:g.23203692C>T
NC_000013.10:g.23777831C>T
CM000675.1:g.23777831C>T
NC_000013.9:g.22675831C>T
NG_008759.1:g.27772C>T
ENST00000218867.4:c.1-3C>T
ENST00000218867.3:c.1-3C>T
NM_000231.2:c.1-3C>T
NM_001378244.1:c.55-3C>T
NM_001378245.1:c.1-3C>T
NM_001378246.1:c.1-3C>T
More

Likely Benign

Met criteria codes 1
BP4
Not Met criteria codes 25
BS2 BS3 BS4 BS1 BP3 BP2 BP1 BP7 BP5 BA1 PS1 PS3 PS2 PS4 PP4 PP1 PP3 PP2 PVS1 PM6 PM2 PM5 PM4 PM1 PM3

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 SGCG 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_000231.3: c.1-3C>T variant is an intronic SGCG variant that is located in a splice region. The computational splicing predictor SpliceAI gives a score of 0.02 for acceptor loss, suggesting that the variant has no impact on splicing since it does not exceed the designated LGMD VCEP threshold (≤0.05) (BP4). The highest minor allele frequency of this variant is 0.0003793 (6/15820 exome chromosomes) in the African/African American population in gnomAD v2.1.1, which is greater than the ClinGen LGMD threshold (≤0.00009) for PM2_Supporting, and therefore does not meet this criterion (PM2_Supporting, BA1, BS1 criteria 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 Limb-Girdle Muscular Dystrophy VCEP (LGMD VCEP specifications version 1.0.0; 01/08/2025): BP4.
Met criteria codes
BP4
The computational splicing predictor SpliceAI gives a score of 0.02 for acceptor loss, suggesting that the variant has no impact on splicing since it does not exceed the designated LGMD VCEP threshold (≤0.05) (BP4).
Not Met criteria codes
BS2
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
BS4
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
BP3
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
BP7
The NM_000231.3: c.1-3C>T variant is an intronic variant that is located in a splice region (BP7 not met).
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
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
PS3
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
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
PVS1
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
The highest minor allele frequency of this variant is 0.0003793 (6/15820 exome chromosomes) in the African/African American population in gnomAD v2.1.1, which is greater than the ClinGen LGMD threshold (≤0.00009) for PM2_Supporting, and therefore does not meet this criterion (no criteria met).
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
PM1
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
Curation History
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