chr15-42396883-T-A

Position:

• chr15-42396883-T-A

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM2 PP3 PP5_Very_Strong

The NM_000070.3(CAPN3):​c.1193+6T>A variant causes a splice donor region, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★).

• Frequency: Genomes: not found (cov: 31)
• Consequence: CAPN3 NM_000070.3 splice_donor_region, intron
• Scores: Splicing: ADA: 0.6594
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:4 O:1
• Conservation: PhyloP100: 0.580

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 Pathogenic. Variant got 11 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_RF, max_spliceai. No scorers claiming Uncertain. Scorers claiming Benign: dbscSNV1_ADA.
• PP5: Variant 15-42396883-T-A is Pathogenic according to our data. Variant chr15-42396883-T-A is described in ClinVar as [Pathogenic]. Clinvar id is 813980.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr15-42396883-T-A is described in Lovd as [Pathogenic]. Variant chr15-42396883-T-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CAPN3	NM_000070.3	c.1193+6T>A		splice_donor_region_variant, intron_variant		ENST00000397163.8
CAPN3	NM_024344.2	c.1193+6T>A		splice_donor_region_variant, intron_variant
CAPN3	NM_173087.2	c.1049+6T>A		splice_donor_region_variant, intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CAPN3	ENST00000397163.8	c.1193+6T>A		splice_donor_region_variant, intron_variant		1	NM_000070.3	P2

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 28

GnomAD4 genome Cov.: 31

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:4 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Autosomal recessive limb-girdle muscular dystrophy type 2A Pathogenic:2 Other:1

Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Oct 13, 2023	This sequence change falls in intron 9 of the CAPN3 gene. It does not directly change the encoded amino acid sequence of the CAPN3 protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or disrupted protein product. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with autosomal recessive limb-girdle muscular dystrophy 2A (LGMD2A) (PMID: 17994539, 20635405). ClinVar contains an entry for this variant (Variation ID: 813980). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in a 31 base pair insertion in intron 9 leading to alternate splicing and introduces a premature termination codon (PMID: 20635405). The resulting mRNA is expected to undergo nonsense-mediated decay. For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, criteria provided, single submitter	research	Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	Apr 11, 2024	The homozygous c.1193+6T>A variant in CAPN3 was identified by our study in one individual with Limb-Girdle Muscular Dystrophy (LGMD). The c.1193+6T>A variant has been reported in >10 individuals with limb-girdle muscular dystrophy (PMID: 22486197, 17994539, 20635405, 30028523), segregated with disease in 5 affected relatives from 1 family (22486197), and absent from large population studies. This variant has also been reported in ClinVar (Variation ID: 813980) and has been interpreted as pathogenic by Women's Health and Genetics/Laboratory Corporation of America (LabCorp), Invitae, and CeGaT Center for Human Genetics Tuebingen. Of the 12 affected individuals, five of those were homozygotes and 5 were compound heterozygotes that carried a reported pathogenic variant in trans or with unknown phase, which increases the likelihood that the c.1193+6T>A variant is pathogenic (Variation ID: 17622, 282173, 217154, 166790; PMID: 22486197, 17994539, 20635405, 30028523). 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. RT-PCR analysis performed on affected tissue shows possible evidence of intron retention after exon 9 (PMID: 20635405). In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive Limb-Girdle Muscular Dystrophy. ACMG/AMP Criteria applied: PP1_strong, PM3_strong, PVS1_strong, PM2_supporting (Richards 2015). -
not provided, no classification provided	literature only	GeneReviews	-	Pathogenic variant most likely the result of a founder effect followed by the Mocheni community in the Fersina River valley in the Italian Alps [Fanin et al 2012]. -

Autosomal recessive limb-girdle muscular dystrophy Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

May 04, 2023

Variant summary: CAPN3 c.1193+6T>A 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. Several computational tools predict a significant impact on normal splicing: Three predict the variant weakens the canonical 5' donor site. At least one publication reports experimental evidence that this variant affects splicing by inserting 31 base pair in the intron 9 which introduces a premature termination codon (example: Nascimbeni_2010). The variant was absent in 251312 control chromosomes (gnomAD). c.1193+6T>A has been reported in the literature in multiple bi-allelic individuals affected with Limb-Girdle Muscular Dystrophy, Autosomal Recessive (example: Guglieri_2008, Nascimbeni_2010, and Fanin_2012). These data indicate that the variant is very likely to be associated with disease. The following publications have been ascertained in the context of this evaluation (PMID: 17994539, 20635405, 22486197). Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as pathogenic (n=2) and VUS (n=1). Based on the evidence outlined above, the variant was classified as pathogenic. -

not provided Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jan 01, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.20
CADD	Benign	17
DANN	Benign	0.93

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.66
dbscSNV1_RF	Pathogenic	0.73
SpliceAI score (max)		0.68		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.68		Position offset: 25
DS_DL_spliceai		0.21		Position offset: -6

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

Publications

LitVar

Other links and lift over

dbSNP: rs1555421532; hg19: chr15-42689081;