rs193922837

chr19-38523211-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 1P and 1B. PP5 BP4

The NM_000540.3(RYR1):c.10348-6C>G variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000266 in 1,614,248 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.000085 (0 hom., cov: 31)
  • Exomes 𝑓: 0.000021 (0 hom.)
• Consequence: RYR1 NM_000540.3 splice_region, splice_polypyrimidine_tract, intron
• Scores: Splicing: ADA: 0.0001551
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:12 U:1 O:1
• Conservation: PhyloP100: -0.101

Genes affected

RYR1 (HGNC:10483): (ryanodine receptor 1) This gene encodes a ryanodine receptor found in skeletal muscle. The encoded protein functions as a calcium release channel in the sarcoplasmic reticulum but also serves to connect the sarcoplasmic reticulum and transverse tubule. Mutations in this gene are associated with malignant hyperthermia susceptibility, central core disease, and minicore myopathy with external ophthalmoplegia. Alternatively spliced transcripts encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PP5: Variant 19-38523211-C-G is Pathogenic according to our data. Variant chr19-38523211-C-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 132994.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=1, Pathogenic=11, Likely_pathogenic=1, not_provided=1}. Variant chr19-38523211-C-G is described in Lovd as [Pathogenic].
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).. Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RYR1	NM_000540.3	c.10348-6C>G		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		ENST00000359596.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RYR1	ENST00000359596.8	c.10348-6C>G		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant		5	NM_000540.3	A2

Frequencies

GnomAD3 genomes AF: 0.0000854 AC: 13 AN: 152242 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.000313

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000199 AC: 5 AN: 251458 Hom.: 0 AF XY: 0.0000147 AC XY: 2 AN XY: 135912

Gnomad AFR exome AF: 0.000246

Gnomad AMR exome AF: 0.0000289

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000205 AC: 30 AN: 1461888 Hom.: 0 Cov.: 33 AF XY: 0.0000165 AC XY: 12 AN XY: 727244

Gnomad4 AFR exome AF: 0.000627

Gnomad4 AMR exome AF: 0.0000224

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.000116

GnomAD4 genome AF: 0.0000853 AC: 13 AN: 152360 Hom.: 0 Cov.: 31 AF XY: 0.000121 AC XY: 9 AN XY: 74496

Gnomad4 AFR AF: 0.000313

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

Bravo AF: 0.000113

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:12 Uncertain:1 Other:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Pathogenic:4 Other:1

Pathogenic, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	Sep 15, 2015	- -
not provided, no classification provided	literature only	Leiden Muscular Dystrophy (RYR1)	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Nov 09, 2022	Reported previously in multiple unrelated individuals with congenital myopathy who also harbored at least one additional RYR1 variant, although phase is not always known (Monnier et al., 2008; Wilmshurst et al., 2010; Bharucha-Goebel et al., 2013; Maggi et al., 2013; Abath Neto et al., 2017; Klein et al., 2012); Published functional studies are suggestive of aberrant splicing (Monnier et al., 2008); In silico analysis is inconclusive as to whether the variant alters gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown.; This variant is associated with the following publications: (PMID: 25525159, 30932294, 21062345, 16380615, 18765655, 30611313, 23919265, 16917943, 23553484, 20583297, 22473935, 20839240, 23394784, 18253926, 28818389, Bhanudeep2021[Article], 34440373) -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jan 01, 2020	- -
Pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Aug 15, 2017	- -

RYR1-related disorder Pathogenic:3

Pathogenic, criteria provided, single submitter	research	Division of Human Genetics, National Health Laboratory Service/University of the Witwatersrand	Jul 01, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	Invitae	Jan 11, 2024	This sequence change falls in intron 68 of the RYR1 gene. It does not directly change the encoded amino acid sequence of the RYR1 protein. RNA analysis indicates that this variant induces altered splicing and may result in an absent or disrupted protein product. This variant is present in population databases (rs193922837, gnomAD 0.03%). This variant has been observed in individual(s) with congenital myopathy (PMID: 18253926, 20839240, 21062345). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 132994). Studies have shown that this variant results in retention of intron 68 and introduces a premature termination codon (PMID: 18253926). 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	clinical testing	Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego	-	This variant affects the canonical splice acceptor site of intron 68 and is therefore predicted to interfere with splicing and result in loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay (NMD). This variant has been previously reported as a compound heterozygous change in patients with congenital myopathy with cores and centronuclear myopathy (PMID: 18253926, 28818389, 30932294, 31069529, 34440373). This variant, in cis with the c.14524G>A (p.Val4842Met) variant, is part of a known haplotype and has been reported as a compound heterozygous change in individuals with RYR1-related myopathies (PMID: 18253926, 20839240). Functional studies demonstrated that the c.10348-6C>G variant resulted in aberrant splicing that introduces a premature termination codon causing the mRNA to undergo NMD (PMID: 18253926, 25525159). The c.10348-6C>G variant is present in the heterozygous state in the gnomAD population database at a frequency of 0.003% (9/282854) and is absent in the homozygous state, thus is presumed to be rare. Based on the available evidence, the c.10348-6C>G variant is classified as Pathogenic. -

Central core myopathy Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Nov 03, 2022	The c.10348-6C>G variant in RYR1 has been reported in the compound heterozygous state in at least 11 individuals of African descent in cis with p.Val4842Met (suggesting it is a founder variant in Africans) and 2 Chilean individuals with congenital myopathy, and segregated with disease in 4 affected relatives from 2 families (Bharucha-Goebel 2013 PMID: 23553484, Wilmshurst 2010 PMID: 20839240, Monnier 2008 PMID: 18253926, Bevilacqua 2011 PMID: 21062345). It has been reported in ClinVar (Variation ID 132994) and has also been identified in 13/41476 of African chromosomes by gnomAD (http://gnomad.broadinstitute.org). In vitro functional studies (using patient tissue) showed that the c.10348-6C>G variant resulted in a loss of splicing of intron 68 and the introduction of a premature stop codon (p.His3449ins33fsX54). Both unspliced and spliced transcripts were present, thus indicating an incomplete penetrance of this intronic variation (Monnier 2008 PMID: 18253926, Bevilacqua 2011 PMID: 1062345). In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive congenital myopathy. ACMG/AMP Criteria applied: PM2_Supporting, PS3_Supporting, PM3_Very strong, PP1. -
Pathogenic, criteria provided, single submitter	research	HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology	Oct 13, 2021	ACMG codes: PS3; PS4M; PM2; PM3; PP5 -

Inborn genetic diseases Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Mar 31, 2016

- -

King Denborough syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

curation

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

Jan 29, 2020

The c.10348-6C>G variant in RYR1 has been reported in at least 16 individuals of African descent in cis with p.Val4842Met (suggesting it is a founder variant in Africans) and 2 Chilean individuals with congenital myopathy, segregated with disease in 4 affected relatives from 2 families (PMID: 23553484, 20839240, 18253926, 21062345), and has been identified in 0.03204% (8/24966) of African chromosomes and 0.002822% (1/35438) of Latino chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs193922837). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. This variant has also been reported pathogenic and likely pathogenic in ClinVar (Variation ID: 132994). In vitro functional studies provide some evidence that the c.10348-6C>G variant may slightly impact normal splicing and protein levels (PMID: 18253926, 21062345). However, these types of assays may not accurately represent biological function. Computational prediction tools, including splice predictors, and conservation analyses suggest that this variant may not impact the protein, though this information is not predictive enough to rule out pathogenicity. The presence of this variant in combination with loss of function variants and in at least 12 individuals with congenital myopathy increases the likelihood that the c.10348-6C>G variant is pathogenic (PMID: 23553484, 20839240, 18253926, 21062345). In summary, this variant meets criteria to be classified as pathogenic for congenital myopathy in an autosomal recessive manner based on multiple occurrences with loss of function variants in affected individuals and low prevalence in the general population. ACMG/AMP Criteria applied: PM3_VeryStrong, PM2, BP4, BP7, PP1, PS3_Supporting (Richards 2015). -

Congenital myopathy with fiber type disproportion;C0751951:Central core myopathy;C1840365:King Denborough syndrome;C1850674:Congenital multicore myopathy with external ophthalmoplegia;C2930980:Malignant hyperthermia, susceptibility to, 1 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Sep 27, 2021

- -

Malignant hyperthermia, susceptibility to, 1 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

All of Us Research Program, National Institutes of Health

Nov 20, 2023

This variant causes a C to G nucleotide substitution at the -6 position of intron 68 of the RYR1 gene. To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with RYR1-related disorders in the literature. This variant has been identified in 9/282854 chromosomes in the general population by the Genome Aggregation Database (gnomAD). This variant has not been reported in individuals affected with autosomal dominant malignant hyperthermia in the literature, although it is associated with other phenotype(s) (ClinVar variation ID: 132994). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	7.2
Dann	Benign	0.66

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.00016
dbscSNV1_RF	Benign	0.13
SpliceAI score (max)		0.47		Details are displayed if max score is > 0.2
DS_AL_spliceai		0.47		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: rs193922837; hg19: chr19-39013851;