rs919322708

Positions:

• chr19-38463527-G-A
• chr19-38463527-G-C
• chr19-38463527-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PP3 PP5

The NM_000540.3(RYR1):​c.2682G>A​(p.Pro894=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000103 in 1,458,930 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: not found (cov: 30)
  • Exomes 𝑓: 0.000010 (0 hom.)
• Consequence: RYR1 NM_000540.3 splice_region, synonymous
• Scores: Splicing: ADA: 0.9995
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:4 U:1
• Conservation: PhyloP100: -0.276

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 2 ACMG points.

• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF, max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 19-38463527-G-A is Pathogenic according to our data. Variant chr19-38463527-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 432001.We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=4, Uncertain_significance=1}.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RYR1	NM_000540.3	c.2682G>A	p.Pro894=	splice_region_variant, synonymous_variant	21/106	ENST00000359596.8	NP_000531.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RYR1	ENST00000359596.8	c.2682G>A	p.Pro894=	splice_region_variant, synonymous_variant	21/106	5	NM_000540.3	ENSP00000352608	A2
RYR1	ENST00000355481.8	c.2682G>A	p.Pro894=	splice_region_variant, synonymous_variant	21/105	1		ENSP00000347667	P4
RYR1	ENST00000599547.6	c.2682G>A	p.Pro894=	splice_region_variant, synonymous_variant, NMD_transcript_variant	21/80	2		ENSP00000471601

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD3 exomes AF: 0.00000406 AC: 1 AN: 246042 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 133740

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

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: 0.000166

GnomAD4 exome AF: 0.0000103 AC: 15 AN: 1458930 Hom.: 0 Cov.: 32 AF XY: 0.0000124 AC XY: 9 AN XY: 725856

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

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: 0.0000108

Gnomad4 OTH exome AF: 0.0000497

GnomAD4 genome Cov.: 30

Bravo AF: 0.00000756

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:4 Uncertain:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Pathogenic:2

Likely pathogenic, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	Jun 23, 2023	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Apr 10, 2023	Identified along with another RYR1 variant in multiple individuals with congenital myopathy or multiminicore disease in published literature; however, phase was not determined and the other variants are not classified as pathogenic (Snoeck et al., 2015; Gonorazky et al., 2019); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports a deleterious effect on splicing; This variant is associated with the following publications: (PMID: 30827497, 25960145, 36131268) -

RYR1-related disorder Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 19, 2023

This sequence change affects codon 894 of the RYR1 mRNA. It is a 'silent' change, meaning that it does not 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 (no rsID available, gnomAD no frequency). This variant has been observed in individuals with clinical features of autosomal recessive RYR1-related conditions (PMID: 30827497). ClinVar contains an entry for this variant (Variation ID: 432001). 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 activation of a cryptic splice site and introduces a premature termination codon (PMID: 30827497). The resulting mRNA is expected to undergo nonsense-mediated decay. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. -

RYR1-related myopathy Pathogenic:1

Likely pathogenic, criteria provided, single submitter

curation

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

Jan 24, 2023

The heterozygous p.Pro894= variant in RYR1 was identified by our study, in the compound heterozygous state with a variant of uncertain significance (ClinVar Variation ID: 159837), in one individual with centronuclear myopathy. This individual also carried a variant of uncertain significance (ClinVar Variation ID: 159837), however, the phase of these variants is unknown at this time. The p.Pro894= variant in in RYR1 has been reported in two unrelated individuals with myopathy (PMID: 25960145, PMID: 30827497), segregated with disease in three affected relatives from one families (PMID: 30827497), but has been identified in 0.0004% (1/246042) of chromosomes by the Genome Aggregation Consortium (gnomAD, http://gnomad.broadinstitute.org; dbSNP ID: rs919322708). Although this variant has been seen in the general population in a heterozygous state, its frequency is low enough to be consistent with a recessive carrier frequency. The p.Pro894= variant in RYR1 has also been reported in ClinVar (Variation ID: 432001) and has been interpreted as pathogenic by Royal Perth Hospital Neurogenetics Laboratory and as a variant of uncertain significance (VUS) by Invitae. RNAseq analysis performed on affected muscle tissue shows altered splicing at the donor splice site of exon 21 and activation of two alternative cryptic donor splice sites, each of which leading to a frameshift, resulting in an overall 2.1-fold decrease in RYR1 expression in affected tissue versus controls (PMID: 30827497). Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. In summary, although additional studies are required to fully establish its clinical significance, this variant is likely pathogenic for autosomal recessive centronuclear myopathy. ACMG/AMP Criteria applied: PS3, PM2_Supporting, PP1, PP3 (Richards 2015). -

Malignant hyperthermia, susceptibility to, 1 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

All of Us Research Program, National Institutes of Health

May 16, 2023

This synonymous variant alters the conserved c.G at the last nucleotide of exon 21 of the RYR1 gene. Splice site prediction tools suggest that this variant may have a significant impact on RNA splicing, this variant is expected to result in an absent or disrupted protein product. This variant has not been reported in individuals affected with malignant hyperthermia susceptibility in the literature. Loss of RYR! function due to haploinsufficiency is not an established disease mechanism for autosomal dominant malignant hyperthermia, although it has been associated with other phenotypes (ClinVar Variation ID: 432001). This variant has been identified in 1/246042 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Due to insufficient evidence, this variant is classified as a Variant of Uncertain Significance for autosomal dominant malignant hyperthermia. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Uncertain	23
DANN	Benign	0.87

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.98
SpliceAI score (max)		0.68		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.28		Position offset: 44
DS_DL_spliceai		0.68		Position offset: 0

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

Publications

LitVar

Other links and lift over

dbSNP: rs919322708; hg19: chr19-38954167; COSMIC: COSV62109305; COSMIC: COSV62109305;