Submissions for variant NM_000070.3(CAPN3):c.1746-20C>G

gnomAD frequency: 0.00320  dbSNP: rs201892814

Total submissions: 13

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
ClinGen Limb Girdle Muscular Dystrophy Variant Curation Expert Panel, ClinGen	RCV003225929	SCV005620237	pathogenic	Autosomal recessive limb-girdle muscular dystrophy	2025-01-09	reviewed by expert panel	curation	The NM_000070.3: c.1746-20C>G variant occurs in intron 13 of the CAPN3 gene. The filtering allele frequency for this variant is 0.006051 in gnomAD v2.1.1 European (non-Finnish) genomes (the lower threshold of the 95% CI of 172/31388), which is higher than the LGMD VCEP threshold of 0.001 for BS1; in total, three homozygous individuals are also observed. However, this variant may act as a hypomorphic allele, and the VCEP opted not to apply this code (BS1 exception). RNAseq/cDNA analysis of muscle from patients carrying one copy of the variant suggests that it results in aberrant splicing, the inclusion of various portions of intron 13, and premature truncation (PMID: 20635405, 35731190). An earlier study concluded the variant does not affect splicing (PMID: 17979987); however, later investigations showed that the aberrantly spliced transcripts are variably expressed and not always detectable even when splicing-specific PCR is used, possibly due to nonsense-mediated mRNA decay (PMID: 20635405) (PVS1_RNA_Moderate). The c.1746-20C>G variant has been detected with a second CAPN3 variant in at least 34 individuals with LGMD (PMID: 37589857, 20635405, 17979987, 17157502, 35731190), including confirmed in trans with a pathogenic variant in five cases (c.550delA p.(Thr184ArgfsTer36), 4.0 pts, PMID: 20635405, 35731190; c.643_663del p.(Ser215_Gly221del): 1.0 pt, PMID: 35731190) (PM3_Very Strong). The variant was also reported to co-segregate with autosomal recessive disease in four affected family members from three families (PP1_Moderate; PMID: 37589857, 20635405, 35731190). Several patients with the c.1746-20C>G variant and a second CAPN3 variant displayed progressive limb girdle muscle weakness or clinical suspicion of limb-girdle muscular dystrophy as well as significantly reduced or absent expression of calpain-3, which is specific for CAPN3-related LGMD (PP4_Moderate; PMID: 20635405). While two homozygous patients with a mild phenotype have been reported (PMID: 35731190), the number of apparently unaffected homozygous individuals described and present in population databases suggests this variant may show reduced penetrance in the homozygous state. In summary, this variant meets the criteria to be classified as Pathogenic 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): PVS1_RNA_Moderate, PM3_Very Strong, PP1_Moderate, PP4_Moderate. The LGMD VCEP recommends careful correlation with patient phenotype and family history as well as consideration of the combined functional impact of both CAPN3 alleles when the c.1746-20C>G variant is detected in an individual with signs of limb girdle muscular dystrophy.
Eurofins Ntd Llc (ga)	RCV000078089	SCV000109927	likely benign	not specified	2016-11-23	criteria provided, single submitter	clinical testing
GeneDx	RCV000585323	SCV000568286	likely benign	not provided	2018-06-06	criteria provided, single submitter	clinical testing	This variant is associated with the following publications: (PMID: 18055493, 28877744, 20635405, 17994539, 17979987, 17157502, 16141003, 16411092, 15351423, 16372320, 27447704, 27708273, 26886200, 27884173, 26301378, 28602176, 25135358, 18854869, 30028523, 30919934, 31788660, 32403337, 31127727)
Labcorp Genetics (formerly Invitae), Labcorp	RCV000559180	SCV000645480	benign	Autosomal recessive limb-girdle muscular dystrophy type 2A	2025-02-02	criteria provided, single submitter	clinical testing
CeGaT Center for Human Genetics Tuebingen	RCV000585323	SCV000692807	benign	not provided	2022-10-01	criteria provided, single submitter	clinical testing	CAPN3: BS1, BS2
Counsyl	RCV000559180	SCV000796481	uncertain significance	Autosomal recessive limb-girdle muscular dystrophy type 2A	2017-12-18	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000078089	SCV002074538	benign	not specified	2022-01-06	criteria provided, single submitter	clinical testing	Variant summary: CAPN3 c.1746-20C>G alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 4/4 computational tools predict no significant impact on normal splicing. This is confirmed by one study reporting no impact on splicing (example, Krahn_2007). In another study. the average value for amount of CAPN3 transcripts relative to three housekeeping genes using CAPN3 mRNA of a patient without splice variant as calibrator, showed the levels of transcript in a patient with this variant in a compound heterozygous genotype did not differ significantly from the control values (example, Stehlikova_2007). The variant allele was found at a frequency of 0.0031 in 251486 control chromosomes, predominantly at a frequency of 0.0043 within the Non-Finnish European subpopulation in the gnomAD database, including 2 homozygotes. This variant is among those re-classified as benign based on lack of phenotype in homozygotes (ACMG BS2-only variants) (example, Abouelhoda_2016). The observed variant frequency within Non-Finnish European control individuals in the gnomAD database is approximately 1.3 fold of the estimated maximal expected allele frequency for a pathogenic variant in CAPN3 causing Limb-Girdle Muscular Dystrophy, Autosomal Recessive phenotype (0.0032), strongly suggesting that the variant is a benign polymorphism found primarily in populations of Non-Finnish European origin. c.1746-20C>G has been reported in the literature as a non-informative genotype in numerous compound heterozygous patients undergoing testing for limb girdle muscular dystrophy via panel/exome/single gene analysis (example, Piluso_2005, Krahn_2007, Stehlikova_2007, Nascimbeni_2010, Avila_2015, Harris_2017, Reddy_2017). In at-least one of these reports it was found to co-occur in cis with a different allele (c.1745+4_1745+7delAGTG) that was characterized by complementary DNA analysis as having a pathogenic outcome (example, Krahn_2007). These report(s) do not provide unequivocal conclusions about association of the variant with Limb-Girdle Muscular Dystrophy type 2A, Autosomal Recessive. To our knowledge, no variant specific experimental evidence demonstrating an impact on protein function has been reported. Seven clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Multiple laboratories reported the variant with conflicting assessments. Based on the evidence outlined above, the variant was classified as benign.
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	RCV003225929	SCV003922315	uncertain significance	Autosomal recessive limb-girdle muscular dystrophy	2023-05-02	criteria provided, single submitter	curation	The heterozygous c.1746-20C>G variant in CAPN3 was identified by our study, in the compound heterozygous state with a pathogenic variant (ClinVar Variation ID: 166786) in one individual with limb girdle muscular dystrophy (Broad Institute Rare Genomes Project). Familial exome analysis revealed that this variant was in trans with a pathogenic variant (ClinVar Variation ID: 166786). The c.1746-20C>G variant in CAPN3 has been previously reported in 19 individuals with autosomal recessive limb-girdle muscular dystrophy 1 (PMID: 30028523, PMID: 27708273, PMID: 27447704, PMID: 28877744, PMID: 28602176, PMID: 26886200, PMID: 18854869, PMID: 18055493, PMID: 16141003, PMID: 17994539, PMID: 16411092, PMID: 17157502, PMID: 17979987) and segregated with disease in two affected individuals from one family (PMID: 27708273), but has been identified in 1.1% (122/10614) of European (non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP ID: rs201892814). This variant has been seen in the general population, in a heterozygous state, at greater rate than expected for disorder. This variant has also been reported in ClinVar (Variation ID: 92408) and has conflicting interpretations. Of the 19 affected individuals reported (PMID: 30028523, PMID: 27708273, PMID: 27447704, PMID: 28877744, PMID: 28602176, PMID: 26886200, PMID: 18854869, PMID: 18055493, PMID: 16141003, PMID: 17994539, PMID: 16411092, PMID: 17157502, PMID: 17979987), one was a homozygote (PMID: 16411092), six were compound heterozygotes who carried pathogenic or likely pathogenic variants in trans (PMID: 18854869, ClinVar Variation ID: 17621, ClinVar Variation ID: 282783; PMID: 26886200, ClinVar Variation ID: 282783; PMID: 28877744, ClinVar Variation ID: 197624; PMID: 2744770, ClinVar Variation ID: 282783, ClinVar Variation ID: 166786), three were presumed compound heterozygotes who carried pathogenic or likely pathogenic variants in unknown phase (PMID: 17157502, ClinVar Variation ID: 166786; PMID: 28602176, PMID: 30028523, ClinVar Variation ID: 813980) and four were compound heterozygotes who carried variants of uncertain significance in trans (PMID: 17994539, PMID: 18854869; PMID: 27708273), which increases the likelihood that the c.1746-20C>G variant is pathogenic. RT-PCR analyses performed on affected tissue are conflicting regarding whether this variant impacts splicing (PMID: 17979987, PMID: 20635405). This variant is located in the 3’ splice region. Computational tools do suggest an impact to splicing. However, this information is not predictive enough to determine pathogenicity. In summary, the clinical significance of the c.1746-20C>G variant is uncertain. ACMG/AMP Criteria applied: PM3_VeryStrong, BS1, PP1_moderate (Richards 2015).
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	RCV000585323	SCV004026401	uncertain significance	not provided	2023-05-31	criteria provided, single submitter	clinical testing	PP4, PS3
Institute of Human Genetics, University Hospital Muenster	RCV004797780	SCV005419367	uncertain significance	See cases	2024-07-15	criteria provided, single submitter	clinical testing	ACMG categories: PM3,BS2
Athena Diagnostics	RCV000585323	SCV005622169	uncertain significance	not provided	2024-02-13	criteria provided, single submitter	clinical testing	Available data are insufficient to determine the clinical significance of the variant at this time. The frequency of this variant in the general population is higher than would generally be expected for pathogenic variants in this gene (Genome Aggregation Database (gnomAD), Cambridge, MA (URL: http://gnomad.broadinstitute.org)). This variant appears to segregate with autosomal recessive LGMD in at least one family. CAPN3 protein was found to be absent or significantly reduced in samples taken from multiple individuals carrying this variant (PMID: 34720847, 20635405). In multiple individuals presenting with LGMD, this variant has been seen with a single recessive pathogenic variant in the same gene, suggesting this variant may be pathogenic (PMID: 34720847, 27447704, 24803842). However, this variant has also been detected homozygous in reportedly healthy individuals (PMID: 27884173). Computational tools yielded predictions that this variant is unlikely to have an effect on normal RNA splicing. Experimental evidence regarding the impact of this variant on splicing is conflicting. This variant has been reported to alter normal mRNA splicing in some publications (PMID: 20635405, 34863162), yet not in another (PMID: 17979987). However, all of these studies have methodological limitations and cannot be viewed as providing conclusive results.
Centre for Mendelian Genomics, University Medical Centre Ljubljana	RCV000626578	SCV000747279	pathogenic	Elevated circulating creatine kinase concentration; Migraine; Difficulty walking; Positive Romberg sign; Paresthesia; EMG: neuropathic changes; Progressive spinal muscular atrophy; Absent muscle fiber calpain-3	2017-01-01	flagged submission	clinical testing
Natera, Inc.	RCV000559180	SCV001460840	uncertain significance	Autosomal recessive limb-girdle muscular dystrophy type 2A	2020-04-17	no assertion criteria provided	clinical testing