rs201892814

chr15-42403721-C-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_000070.3(CAPN3):c.1746-20C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0031 in 1,612,376 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.0031 (1 hom., cov: 32)
  • Exomes 𝑓: 0.0031 (14 hom.)
• Consequence: CAPN3 NM_000070.3 intron
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1 U:4 B:5
• Conservation: PhyloP100: 0.0590

Genes affected

CAPN3 (HGNC:1480): (calpain 3) Calpain, a heterodimer consisting of a large and a small subunit, is a major intracellular protease, although its function has not been well established. This gene encodes a muscle-specific member of the calpain large subunit family that specifically binds to titin. Mutations in this gene are associated with limb-girdle muscular dystrophies type 2A. Alternate promoters and alternative splicing result in multiple transcript variants encoding different isoforms and some variants are ubiquitously expressed. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BS2: High Homozygotes in GnomAdExome at 3 AD,AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAPN3	NM_000070.3	c.1746-20C>G		intron_variant		ENST00000397163.8
CAPN3	NM_024344.2	c.1746-20C>G		intron_variant
CAPN3	NM_173087.2	c.1602-20C>G		intron_variant
CAPN3	NM_173088.2	c.210-20C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAPN3	ENST00000397163.8	c.1746-20C>G		intron_variant		1	NM_000070.3	P2

Frequencies

GnomAD3 genomes AF: 0.00309 AC: 470 AN: 152174 Hom.: 1 Cov.: 32

Gnomad AFR AF: 0.000459

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000524

Gnomad ASJ AF: 0.00202

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.0115

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.00453

Gnomad OTH AF: 0.00191

GnomAD3 exomes AF: 0.00315 AC: 791 AN: 251486 Hom.: 3 AF XY: 0.00324 AC XY: 441 AN XY: 135918

Gnomad AFR exome AF: 0.000246

Gnomad AMR exome AF: 0.00119

Gnomad ASJ exome AF: 0.00208

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000653

Gnomad FIN exome AF: 0.0100

Gnomad NFE exome AF: 0.00426

Gnomad OTH exome AF: 0.00342

GnomAD4 exome AF: 0.00311 AC: 4534 AN: 1460084 Hom.: 14 Cov.: 30 AF XY: 0.00312 AC XY: 2268 AN XY: 726476

Gnomad4 AFR exome AF: 0.000179

Gnomad4 AMR exome AF: 0.00105

Gnomad4 ASJ exome AF: 0.00253

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.0000464

Gnomad4 FIN exome AF: 0.00983

Gnomad4 NFE exome AF: 0.00335

Gnomad4 OTH exome AF: 0.00254

GnomAD4 genome AF: 0.00309 AC: 470 AN: 152292 Hom.: 1 Cov.: 32 AF XY: 0.00314 AC XY: 234 AN XY: 74466

Gnomad4 AFR AF: 0.000457

Gnomad4 AMR AF: 0.000523

Gnomad4 ASJ AF: 0.00202

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.0115

Gnomad4 NFE AF: 0.00453

Gnomad4 OTH AF: 0.00189

Alfa AF: 0.00420 Hom.: 0

Bravo AF: 0.00209

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:1 Uncertain:4 Benign:5

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Autosomal recessive limb-girdle muscular dystrophy type 2A Uncertain:2 Benign:1

Uncertain significance, criteria provided, single submitter	clinical testing	Counsyl	Dec 18, 2017	- -
Benign, criteria provided, single submitter	clinical testing	Invitae	Feb 01, 2024	- -
Uncertain significance, no assertion criteria provided	clinical testing	Natera, Inc.	Apr 17, 2020	- -

not provided Uncertain:1 Benign:2

Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 06, 2018	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) -
Benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Oct 01, 2022	CAPN3: BS1, BS2 -
Uncertain significance, criteria provided, single submitter	clinical testing	Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	May 31, 2023	PP4, PS3 -

not specified Benign:2

Benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jan 06, 2022	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. -
Likely benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Nov 23, 2016	- -

Paresthesia;C0149931:Migraine;C0240914:Positive Romberg sign;C0241005:Elevated circulating creatine kinase concentration;C0311394:Difficulty walking;C4021727:EMG: neuropathic changes;C4022625:Absent muscle fiber calpain-3;C4082951:Progressive spinal muscular atrophy Pathogenic:1

Pathogenic, flagged submission

clinical testing

Centre for Mendelian Genomics, University Medical Centre Ljubljana

Jan 01, 2017

- -

Autosomal recessive limb-girdle muscular dystrophy Uncertain:1

Uncertain significance, criteria provided, single submitter

curation

Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard

May 02, 2023

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). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	1.7
Dann	Benign	0.59

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.13		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs201892814; hg19: chr15-42695919;