NM_000540.3:c.7025A>G

Variant names:

• chr19-38499241-A-G
• rs147213895
• NM_000540.3:c.7025A>G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BS1 BS2

This summary comes from the ClinGen Evidence Repository: The c.7025A>G (NM_000540.3(RYR1):c.7025A>G (p.Asn2342Ser)) variant in RYR1 is a missense variant predicted to cause substitution of asparagine by serine at amino acid 2342 (p.Asn2342Ser). The highest MAF in gnomAD v4.1.0 is 0.001818 (2145/1180004 alleles) in the European (non-Finnish) population, which is greater than the ClinGen Congenital Myopathies VCEP threshold (≥0.000697) for BS1, and therefore meets this criterion (BS1). This variant has been observed in 3 homozygous individuals with no features of RYR1-related myopathy, a condition with full penetrance at an early age (BS2). The computational predictor REVEL gives a score of 0.639, which is neither above nor below the thresholds predicting a damaging or benign impact on RYR1 function. The variant is near the end of the exon, but the highest SpliceAI score is 0.04 for donor gain, and the other scores are 0.00, indicating no significant impact to splicing is predicted (no codes met). This variant was found in six probands from five families (two compound heterozygous and three heterozygous cases). However, none of these probands were scored due to the high population allele frequency, and, in specific cases, a potentially causative RYR1 variant on the same allele, a causative variant in another gene, or lack of phenotypic detail/specificity (no codes met; Synnovis Internal Data; PMIDs: 23826317, 31903994, 38982518). In summary, this variant meets the criteria to be classified as benign for RYR1-related myopathy (undetermined mode of inheritance) based on the ACMG/AMP criteria applied, as specified by theClinGen Congenital Myopathy VCEP: (BS1, BS2; ClinGen Congenital Myopathies VCEP Specifications Version 2.0; 02/10/2025). LINK:https://erepo.genome.network/evrepo/ui/classification/CA024665/MONDO:0100150/150

• Frequency:
  • Genomes: 𝑓 0.0011 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0016 (3 hom.)
• Consequence: RYR1 NM_000540.3 missense, splice_region
• Scores: Splicing: ADA: 0.007624
• Clinical Significance: Benign/Likely benign reviewed by expert panel U:9 B:11 O:2
• Conservation: PhyloP100: 9.32

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 Benign. Variant got -8 ACMG points.

• BS1: For more information check the summary or visit ClinGen Evidence Repository.
• BS2: For more information check the summary or visit ClinGen Evidence Repository.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RYR1	NM_000540.3	c.7025A>G	p.Asn2342Ser	missense_variant, splice_region_variant	Exon 43 of 106	ENST00000359596.8	NP_000531.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RYR1	ENST00000359596.8	c.7025A>G	p.Asn2342Ser	missense_variant, splice_region_variant	Exon 43 of 106	5	NM_000540.3	ENSP00000352608.2
RYR1	ENST00000355481.8	c.7025A>G	p.Asn2342Ser	missense_variant, splice_region_variant	Exon 43 of 105	1		ENSP00000347667.3
RYR1	ENST00000594335.5	n.476A>G		splice_region_variant, non_coding_transcript_exon_variant	Exon 4 of 49	1		ENSP00000470927.2
RYR1	ENST00000599547.6	n.7025A>G		splice_region_variant, non_coding_transcript_exon_variant	Exon 43 of 80	2		ENSP00000471601.2

Frequencies

GnomAD3 genomes AF: 0.00105 AC: 160 AN: 152136 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000410

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000523

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00124

Gnomad FIN AF: 0.000660

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00178

Gnomad OTH AF: 0.000479

GnomAD3 exomes AF: 0.00104 AC: 262 AN: 251376 Hom.: 0 AF XY: 0.00124 AC XY: 169 AN XY: 135888

Gnomad AFR exome AF: 0.000185

Gnomad AMR exome AF: 0.000347

Gnomad ASJ exome AF: 0.0000992

Gnomad EAS exome AF: 0.0000544

Gnomad SAS exome AF: 0.00206

Gnomad FIN exome AF: 0.000416

Gnomad NFE exome AF: 0.00147

Gnomad OTH exome AF: 0.000978

GnomAD4 exome AF: 0.00156 AC: 2278 AN: 1461864 Hom.: 3 Cov.: 32 AF XY: 0.00157 AC XY: 1141 AN XY: 727238

Gnomad4 AFR exome AF: 0.000239

Gnomad4 AMR exome AF: 0.000246

Gnomad4 ASJ exome AF: 0.0000383

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.00160

Gnomad4 FIN exome AF: 0.000599

Gnomad4 NFE exome AF: 0.00182

Gnomad4 OTH exome AF: 0.00103

GnomAD4 genome AF: 0.00105 AC: 160 AN: 152254 Hom.: 0 Cov.: 32 AF XY: 0.000981 AC XY: 73 AN XY: 74440

Gnomad4 AFR AF: 0.000409

Gnomad4 AMR AF: 0.000523

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00124

Gnomad4 FIN AF: 0.000660

Gnomad4 NFE AF: 0.00178

Gnomad4 OTH AF: 0.000474

Alfa AF: 0.00208 Hom.: 2

Bravo AF: 0.000960

TwinsUK AF: 0.00135 AC: 5

ALSPAC AF: 0.00156 AC: 6

ESP6500AA AF: 0.000454 AC: 2

ESP6500EA AF: 0.00128 AC: 11

ExAC AF: 0.00107 AC: 130

Asia WGS AF: 0.000289 AC: 1 AN: 3478

EpiCase AF: 0.00224

EpiControl AF: 0.00130

ClinVar

Significance: Benign/Likely benign

Submissions summary: Uncertain:9 Benign:11 Other:2

Revision: reviewed by expert panel

Submissions by phenotype

Malignant hyperthermia, susceptibility to, 1 Uncertain:3 Benign:5

Sep 23, 2024

All of Us Research Program, National Institutes of Health

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Mar 18, 2021

ClinGen Malignant Hyperthermia Susceptibility Variant Curation Expert Panel, ClinGen

Significance: Likely benign

Review Status: reviewed by expert panel

Collection Method: curation

This pathogenicity assessment is relevant only for malignant hyperthermia susceptibility (MHS) inherited in an autosomal dominant pattern. Variants in RYR1 can also cause other myopathies inherited in an autosomal dominant pattern or in an autosomal recessive pattern. Some of these disorders may predispose individuals to malignant hyperthermia. RYR1 variants may also contribute to a malignant hyperthermia reaction in combination with other genetic and non-genetic factors and the clinician needs to consider such factors in making management decisions. This sequence variant predicts a substitution of asparagine with serine at codon 2342 of the RYR1 protein p.(Asn2342Ser). The maximum allele frequency for this variant among the six major gnomAD populations is SAS: 0.00206, which is considered to be more common than expected for a pathogenic variant causing autosomal dominantly inherited MHS, BS1. This variant has been reported in over ten unrelated individuals who have a personal or family history of a malignant hyperthermia reaction, at least nine of these individuals had a positive in vitro contracture test (IVCT) or caffeine halothane contracture test (CHCT) result (when the proband was unavailable for testing a positive diagnostic test result in a mutation positive relative was counted)( PMID:30236257, PMID:23558838, PMID:24433488, personal communication) However, the high MAF in the NFE population in gnomAD precludes the use of PS4. This variant has been shown to segregate with IVCT status in at least three individuals across two families, PP1 (PMID:30236257, personal communication). In other families at least two genotype positive IVCT negative individuals have been reported, BS2 (PMID:15221887, personal communication). HEK293 assay shows increased sensitivity to 4CmC, PS3_Moderate (PMID: 15221887). A functional study published using B-lymphocytes showed increased acidification rates, however, this assay is not considered a standard assay by the ClinGen RYR1 VCEP for MHS (PMID:19191333). This variant resides in a region of RYR1 considered to be a hotspot for pathogenic variants that contribute to MHS, PM1 (PMID: 21118704). A REVEL score of 0.639 supports neither a pathogenic or a benign status. Criteria implemented include: PS3_Moderate, PM1, PP1, BS1, BS2. Based on using Bayes to combine criteria this variant is assessed as Likely Benign, (PMID: 29300386). -

Jul 01, 2013

Biesecker Lab/Clinical Genomics Section, National Institutes of Health

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: research

- -

Aug 22, 2023

Mendelics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jan 01, 2019

Institute of Human Genetics, University of Leipzig Medical Center

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jul 13, 2022

Color Diagnostics, LLC DBA Color Health

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Jun 01, 2014

CSER _CC_NCGL, University of Washington

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: research

- -

Jul 07, 2023

Molecular Genetics, Royal Melbourne Hospital

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change is predicted to replace asparagine with serine at codon 2342 of the RYR1 protein, p.(Asn2342Ser). The asparagine residue is evolutionarily conserved (100 vertebrates, UCSC), and is located in exon 43 in the central region hotspot of the RYR1 cytosolic shell (amino acids 2,101-2,458). There is a small physicochemical difference between asparagine and serine. The highest population minor allele frequency in gnomAD v3.1 is 0.2% (121/68,012 alleles) in the European (non-Finnish) population. The prevalence of the variant in malignant hyperthermia (MH) susceptible individuals with positive in vitro contracture tests (IVCT) is significantly increased compared with the prevalence in the European (non-Finnish) population (the population with the maximum allele frequency) in gnomAD v3.1 (Odds ratio 3.06, 95% CI:1.64 to 5.68, p=0.0004; PMID: 19191333, 23558838, 25960145, 28224104, 30236257). There is conflicting segregation of the variant in MH susceptible and non-susceptible individuals in multiple families (PMID: 15221887, 20681998, 25960145). The variant demonstrates increased sensitivity to RYR1 agonist in an HEK293 in vitro assay with appropriate controls and in patient cells (PMID: 19191333, 31903994). The variant has been reported in at least two unrelated individuals with a negative IVCT (PMID: 15221887, 20681998). Computational evidence is uninformative for the missense substitution (REVEL = 0.639). Based on the classification scheme RMH Modified ACMG Guidelines v1.6.1, this variant is classified as a VARIANT OF UNCERTAIN SIGNIFICANCE. Following criteria are met: PS3_Moderate, PM1, PS4_Supporting, PP1, BS1, BS2. -

not provided Uncertain:3 Benign:2 Other:1

May 12, 2017

Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

-

RYR1 database

Significance: not provided

Review Status: no classification provided

Collection Method: literature only

- -

Nov 30, 2021

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

See Variant Classification Assertion Criteria. -

Mar 21, 2014

Eurofins Ntd Llc (ga)

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Nov 01, 2024

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

RYR1: PP3, BS2 -

Dec 22, 2022

Revvity Omics, Revvity

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not specified Uncertain:1 Benign:1

May 28, 2024

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

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: RYR1 c.7025A>G (p.Asn2342Ser) results in a conservative amino acid change located in the RIH domain (IPR000699) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. Consensus agreement among computation tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.0015 in 1614118 control chromosomes, predominantly at a frequency of 0.0018 within the South Asian subpopulation in the gnomAD database, including 1 homozygote. The observed variant frequency within South Asian control individuals in the gnomAD database is approximately 21 fold of the estimated maximal expected allele frequency for a pathogenic variant in RYR1 causing Malignant Hyperthermia Susceptibility phenotype (8.8e-05). c.7025A>G has been reported in the literature in individuals affected with malignant hyperthermia susceptibility (example: Carpenter_2009, Schiemann_2020). However, these report(s) do not provide unequivocal conclusions about association of the variant with Malignant Hyperthermia Susceptibility. Co-occurrences with other pathogenic variants have been reported (RYR1 c.1021G>A, p.Gly341Arg; RYR1 c.7063C>T, p.Arg2355Trp), providing supporting evidence for a benign role. In functional calcium release assays, the variant showed increased sensitivity compared to wild-type control cells (Schiemann_2020). The following publications have been ascertained in the context of this evaluation (PMID: 19825159, 31903994). ClinVar contains an entry for this variant (Variation ID: 133175). Based on the evidence outlined above, the variant was classified as likely benign. -

Jan 24, 2017

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: This variant is present in ExAC at a MaxMAF of 0.24% in South Asian chromosomes (including 1 homozygote). It is present in 11 papers in HGMD, most of which classify the variant as a VUS as it has been seen in affected and unaffected patients. It is classified with 1 star in ClinVar as VUS by Emory and CSER and as Likely benign by Biesecker Lab. It is not present in the www.emhg.org RYR1 database. -

RYR1-related disorder Uncertain:1 Benign:1

May 10, 2024

PreventionGenetics, part of Exact Sciences

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

The RYR1 c.7025A>G variant is predicted to result in the amino acid substitution p.Asn2342Ser. This variant has been reported in several individuals with malignant hyperthermia (MH) (see, for example, Marchant et al. 2004. PubMed ID: 15221887; Miller et al. 2018. PubMed ID: 30236257). However, some individuals with MH who carry this variant also had another causative RYR1 variant (Carpenter et al. 2009. PubMed ID: 19825159; Supplementary File 1, Knuiman et al. 2019. PubMed ID: 30788618). In one family, this variant was detected in trans with a clear dominant, pathogenic MH variant in the proband and also observed in the proband’s three children, at least two of whom had negative in vitro contracture testing (Tammaro et al. 2011. PubMed ID: 20681998). This variant is reported in 0.21% of alleles in individuals of South Asian descent in gnomAD v2, which is much more frequent (~10 times) than the most frequent, well-characterized MH pathogenic variants. In the updated gnomAD v4, three individuals homozygous for this variant were observed. The ClinGen Malignant Hyperthermia Susceptibility Variant Curation Expert Panel interprets this variant as likely benign in regard to autosomal dominant malignant hyperthermia susceptibility (https://www.ncbi.nlm.nih.gov/clinvar/variation/133175/). This variant has also been reported with or without a second RYR1 variant in individuals with RYR1-related myopathy (Snoeck et al. 2015. PubMed ID: 25960145; Garibaldi et al. 2019. PubMed ID: 30611313; Fusto et al. 2022. PubMed ID: 35428369). This variant was found in a parent with congenital myopathy; however, it was not found in the individual’s similarly affected daughter, and a TPM3 variant was found in both individuals (Klein et al. 2012. PubMed ID: 22473935). In summary, this variant is likely too common to be a primary cause of RYR1-related disorders and the clinical significance of this variant is uncertain due to conflicting evidence. -

Feb 02, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Centronuclear myopathy Uncertain:1

Mar 01, 2024

Muscle and Diseases Team, Institut de Génétique et Biologie Moléculaire et Cellulaire

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: research

PP1_Strong+PM2+PP2+BS2 -

Malignant hyperthermia of anesthesia Benign:1

Jun 14, 2016

Illumina Laboratory Services, Illumina

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

RYR1-related myopathy Benign:1

Feb 10, 2025

ClinGen Congenital Myopathies Variant Curation Expert Panel, ClinGen

Significance: Benign

Review Status: reviewed by expert panel

Collection Method: curation

The c.7025A>G (NM_000540.3(RYR1):c.7025A>G (p.Asn2342Ser)) variant in RYR1 is a missense variant predicted to cause substitution of asparagine by serine at amino acid 2342 (p.Asn2342Ser). The highest MAF in gnomAD v4.1.0 is 0.001818 (2145/1180004 alleles) in the European (non-Finnish) population, which is greater than the ClinGen Congenital Myopathies VCEP threshold (≥0.000697) for BS1, and therefore meets this criterion (BS1). This variant has been observed in 3 homozygous individuals with no features of RYR1-related myopathy, a condition with full penetrance at an early age (BS2). The computational predictor REVEL gives a score of 0.639, which is neither above nor below the thresholds predicting a damaging or benign impact on RYR1 function. The variant is near the end of the exon, but the highest SpliceAI score is 0.04 for donor gain, and the other scores are 0.00, indicating no significant impact to splicing is predicted (no codes met). This variant was found in six probands from five families (two compound heterozygous and three heterozygous cases). However, none of these probands were scored due to the high population allele frequency, and, in specific cases, a potentially causative RYR1 variant on the same allele, a causative variant in another gene, or lack of phenotypic detail/specificity (no codes met; Synnovis Internal Data; PMIDs: 23826317, 31903994, 38982518). In summary, this variant meets the criteria to be classified as benign for RYR1-related myopathy (undetermined mode of inheritance) based on the ACMG/AMP criteria applied, as specified by the ClinGen Congenital Myopathy VCEP: (BS1, BS2; ClinGen Congenital Myopathies VCEP Specifications Version 2.0; 02/10/2025). -

Congenital myopathy with fiber type disproportion;C1850674:Congenital multicore myopathy with external ophthalmoplegia;C2930980:Malignant hyperthermia, susceptibility to, 1;C5830701:Central core myopathy Other:1

-

GenomeConnect, ClinGen

Significance: not provided

Review Status: no classification provided

Collection Method: phenotyping only

Variant interpretted as Uncertain significance and reported on 02-08-2015 by Lab or GTR ID 26957. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.26
BayesDel_addAF	Benign	-0.25	T
BayesDel_noAF	Benign	-0.12
CADD	Benign	22
DANN	Uncertain	0.99
DEOGEN2	Pathogenic	0.96	.;D
Eigen	Uncertain	0.35
Eigen_PC	Uncertain	0.27
FATHMM_MKL	Pathogenic	1.0	D
LIST_S2	Uncertain	0.96	D;D
M_CAP	Pathogenic	0.54	D
MetaRNN	Benign	0.11	T;T
MetaSVM	Pathogenic	0.91	D
MutationAssessor	Benign	2.0	M;M
PrimateAI	Uncertain	0.74	T
PROVEAN	Pathogenic	-4.6	D;D
REVEL	Uncertain	0.64
Sift	Benign	0.053	T;T
Polyphen		1.0	D;P
Vest4		0.68
MVP		0.98
MPC		0.25
ClinPred		0.11	T
GERP RS		3.7
Varity_R		0.28
gMVP		0.90

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.0076
dbscSNV1_RF	Benign	0.15
SpliceAI score (max)		0.040		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: rs147213895; hg19: chr19-38989881;