rs371147744

Positions:

• chr1-237707023-G-A

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 1P and 7B. PP2 BP4_Moderate BP6 BS2

The NM_001035.3(RYR2):​c.9655G>A​(p.Val3219Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000189 in 1,613,718 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. V3219V) has been classified as Likely benign.

• Frequency:
  • Genomes: 𝑓 0.000099 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00020 (0 hom.)
• Consequence: RYR2 NM_001035.3 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:8 B:4
• Conservation: PhyloP100: 1.32

Genes affected

RYR2 (HGNC:10484): (ryanodine receptor 2) This gene encodes a ryanodine receptor found in cardiac muscle sarcoplasmic reticulum. The encoded protein is one of the components of a calcium channel, composed of a tetramer of the ryanodine receptor proteins and a tetramer of FK506 binding protein 1B proteins, that supplies calcium to cardiac muscle. Mutations in this gene are associated with stress-induced polymorphic ventricular tachycardia and arrhythmogenic right ventricular dysplasia. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• PP2: Missense variant where missense usually causes diseases, RYR2
• BP4: Computational evidence support a benign effect (MetaRNN=0.121982455).
• BP6: Variant 1-237707023-G-A is Benign according to our data. Variant chr1-237707023-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 201179.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=7, Likely_benign=4}. Variant chr1-237707023-G-A is described in Lovd as [Likely_benign].
• BS2: High AC in GnomAd4 at 15 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RYR2	NM_001035.3	c.9655G>A	p.Val3219Met	missense_variant	68/105	ENST00000366574.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RYR2	ENST00000366574.7	c.9655G>A	p.Val3219Met	missense_variant	68/105	1	NM_001035.3	P1
RYR2	ENST00000660292.2	c.9655G>A	p.Val3219Met	missense_variant	68/106
RYR2	ENST00000659194.3	c.9655G>A	p.Val3219Met	missense_variant	68/105
RYR2	ENST00000609119.2	c.*690G>A		3_prime_UTR_variant, NMD_transcript_variant	66/104	5

Frequencies

GnomAD3 genomes AF: 0.0000986 AC: 15 AN: 152088 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000241

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: 0.000206

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000763 AC: 19 AN: 249136 Hom.: 0 AF XY: 0.0000740 AC XY: 10 AN XY: 135154

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000261

Gnomad ASJ exome AF: 0.0000994

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000709

Gnomad OTH exome AF: 0.000165

GnomAD4 exome AF: 0.000198 AC: 290 AN: 1461630 Hom.: 0 Cov.: 31 AF XY: 0.000223 AC XY: 162 AN XY: 727102

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.000224

Gnomad4 ASJ exome AF: 0.0000383

Gnomad4 EAS exome AF: 0.0000252

Gnomad4 SAS exome AF: 0.0000116

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000231

Gnomad4 OTH exome AF: 0.000331

GnomAD4 genome AF: 0.0000986 AC: 15 AN: 152088 Hom.: 0 Cov.: 32 AF XY: 0.0000808 AC XY: 6 AN XY: 74282

Gnomad4 AFR AF: 0.0000241

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: 0.000206

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000135 Hom.: 0

Bravo AF: 0.0000982

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000120 AC: 1

ExAC AF: 0.0000744 AC: 9

EpiCase AF: 0.000218

EpiControl AF: 0.000178

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:8 Benign:4

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not specified Uncertain:2 Benign:1

Likely benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Apr 18, 2023	Variant summary: RYR2 c.9655G>A (p.Val3219Met) results in a conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 7.6e-05 in 249136 control chromosomes (gnomAD). The observed variant frequency is approximately 3 fold of the estimated maximal expected allele frequency for a pathogenic variant in RYR2 causing Cardiomyopathy phenotype (2.5e-05), strongly suggesting that the variant is benign. c.9655G>A has been reported in the literature in individuals affected with presyncope and myocarditis (example: Roux-Buisson_2014 and Seidel_2021). These report(s) do not provide unequivocal conclusions about association of the variant with Cardiomyopathy. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Nine clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as VUS (n=7) and likely benign (n=2). Based on the evidence outlined above, the variant was classified as likely benign. -
Uncertain significance, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Dec 03, 2015	The p.Val3219Met variant in RYR2 has been reported in 1 individual with ARVC (Ro ux-Buisson 2014) and in 5/66632 European chromosomes by the Exome Aggregation Co nsortium (ExAC, http://exac.broadinstitute.org; dbSNP rrs371147744). Computatio nal prediction tools and conservation analysis suggest that the p.Val3219Met var iant may not impact the protein, though this information is not predictive enoug h to rule out pathogenicity. In summary, the clinical significance of the p.Val3 219Met variant is uncertain. -
Uncertain significance, no assertion criteria provided	clinical testing	Stanford Center for Inherited Cardiovascular Disease, Stanford University	Mar 31, 2011	Note this variant was found in clinical genetic testing performed by one or more labs who may also submit to ClinVar. Thus any internal case data may overlap with the internal case data of other labs. The interpretation reviewed below is that of the Stanford Center for Inherited Cardiovascular Disease. p.Val3219Met (V3219M; c.9655 G>A) in the RYR2 gene: Based on the limited data currently available about this variant (reviewed in detail below), we agree and consider this a variant of unknown significance. This variant has been reported just once in the literature, according to our search, by Roux-Buisson et al. (online publication before print, July 2014). No segregation data is available. They found this variant in one Caucasian male proband recruited in France or Switzerland who was borderline for ARVC by 2010 criteria and who had previously tested negative for variants in desmosomal genes associated with ARVC (PKP2, DSG2, DSP, JUP, and DSC2). This was a sporadic case, with no family history of ARVC, who presented with presyncope at the age of 41. Resting EKG showed T wave inversion from lead V1 to lead V3. 24-hour Holter monitoring detected frequent monomorphic ventricular ectopies decreasing during exercise. Cardiac imaging showed wall motion abnormalities with dyskinesia and RV aneurysm but no RV dilatation and therefore did not reach the 2010 diagnostic criteria. This is a conservative amino acid substitution from a nonpolar valine to a nonpolar methionine at a residue that is not conserved across vertebrate species (Ambry lists at least 7 species it differs in including rat and mouse). This valine is not conserved across paralog proteins (RYR1-RYR3; http://cardiodb.org/Paralogue_Annotation/), and nor are several amino acids nearby. In silico analysis with PolyPhen-2 predicts this variant to be “Possibly Damaging” with a score of 0.631. SIFT predicts that it is tolerated, according to Ambry. Yano et al. (2006) reported that disease-causing variants in RYR2 cluster within 3 hot-spot regions: the N-terminal domain (residues 77-433), the central domain (residues 2246-2534), and the C-terminal domain (residues 3778-4959). This variant does not fall within a known disease-causing hotspot. There are no missense variants at nearby residues (+/-10) listed in HGMD in association with CPVT or ARVC (as of January 2014). This variant is listed in dbSNP as rs371147744. It was submitted twice: Once by the NHLBI ESP, and once by a genome sequencing project in the Netherlands. The variant has been seen in 1 out of ~6,200 individuals from controls and individuals from publicly available population datasets. Of note, none of these match the ethnicity of our patients, which is Filipino. It is present in one Caucasian from the NHLBI Exome Sequencing Project dataset, which currently includes variant calls on ~4100 Caucasian and ~1900 African American individuals. The phenotype of those individuals is not publicly available, however the cohorts that were merged to create this dataset were all either general population samples or samples recruited for common cardiovascular disease such as hypertension. Roux-Buisson et al. (2014) did not find it in 200 Caucasian controls. There is no variation at this codon listed in 1000 Genomes (as of November 10, 2014). -

Cardiomyopathy Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Feb 06, 2023	This variant is located in the RYR2 protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with cardiovascular disorders in the literature. This variant has been identified in 21/280528 chromosomes in the general population by the Genome Aggregation Database (gnomAD). 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. -
Uncertain significance, criteria provided, single submitter	clinical testing	CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario	Aug 24, 2017	- -

not provided Uncertain:1 Benign:1

Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Mar 01, 2024	RYR2: BP4 -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Oct 06, 2016	A variant of uncertain significance has been identified in the RYR2 gene. The V3219M variant has previously been reported in a 41 year-old patient who had clinical features consistent with ARVC, but did not meet 2010 Task Force Criteria for a diagnosis of ARVC (Roux-Buisson et al., 2014). This variant has also been observed in other unrelated individuals referred for cardiac genetic testing at GeneDx, and has been classified in ClinVar as a variant of uncertain significance by other clinical laboratories (ClinVar SCV000263004.2, SCV000272400.1, SCV000280458.1; Landrum et al., 2016). The V3219M variant was not observed at a significant frequency in approximately 6,100 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. However, the V3219M variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. This substitution occurs at a position that is not conserved across species, and Methionine is the wild-type amino acid at this position in at least two species. This variant is not located in one of the three hot-spot regions of the RYR2 gene, where the majority of pathogenic missense variants occur (Medeiros-Domingo et al., 2009). Furthermore, 2/3 in silico splice prediction programs predict this variant likely does not alter the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is pathogenic or benign. -

Catecholaminergic polymorphic ventricular tachycardia 1 Benign:2

Likely benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 27, 2017	This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Likely benign, criteria provided, single submitter	clinical testing	Invitae	Jan 29, 2024	- -

Catecholaminergic polymorphic ventricular tachycardia Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

All of Us Research Program, National Institutes of Health

Feb 05, 2024

This variant is located in the RYR2 protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with cardiovascular disorders in the literature. This variant has been identified in 21/280528 chromosomes in the general population by the Genome Aggregation Database (gnomAD). 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. -

Arrhythmogenic right ventricular dysplasia 2 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Apr 27, 2017

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -

Cardiovascular phenotype Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Feb 05, 2024

The p.V3219M variant (also known as c.9655G>A), located in coding exon 68 of the RYR2 gene, results from a G to A substitution at nucleotide position 9655. The valine at codon 3219 is replaced by methionine, an amino acid with highly similar properties. This alteration has been reported in a cohort of subjects referred for arrhythmogenic right ventricular cardiomyopathy (ARVC) genetic testing (Roux-Buisson N et al. Heart Rhythm, 2014 Nov;11:1999-2009). This alteration has also been reported in an exome cohort, but cardiovascular history was not provided (Landstrom AP et al. Circ Arrhythm Electrophysiol, 2017 Apr;10). This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.073
BayesDel_addAF	Benign	-0.26	T
BayesDel_noAF	Benign	-0.32
CADD	Benign	20
DANN	Uncertain	0.99
DEOGEN2	Benign	0.37	T;T
Eigen	Benign	-0.011
Eigen_PC	Benign	0.11
FATHMM_MKL	Uncertain	0.78	D
LIST_S2	Uncertain	0.89	D;D
M_CAP	Benign	0.071	D
MetaRNN	Benign	0.12	T;T
MetaSVM	Benign	-0.39	T
MutationAssessor	Benign	0.60	N;.
MutationTaster	Benign	0.99	N
PrimateAI	Benign	0.48	T
PROVEAN	Benign	-0.23	N;.
REVEL	Benign	0.22
Sift	Benign	0.071	T;.
Polyphen		0.63	P;.
Vest4		0.28
MVP		0.54
MPC		0.37
ClinPred		0.042	T
GERP RS		3.8
Varity_R		0.039
gMVP		0.28

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs371147744; hg19: chr1-237870323; COSMIC: COSV63687970;