rs201500134

chr1-237657976-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 1P and 11B. PP2 BP4_Moderate BP6 BS1 BS2

The NM_001035.3(RYR2):c.8162T>C(p.Ile2721Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0013 in 1,519,710 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I2721L) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.00064 (0 hom., cov: 33)
  • Exomes 𝑓: 0.0014 (6 hom.)
• Consequence: RYR2 NM_001035.3 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:6 B:12
• Conservation: PhyloP100: 2.82

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 Benign. Variant got -10 ACMG points.

• PP2: Missense variant where missense usually causes diseases, RYR2
• BP4: Computational evidence support a benign effect (MetaRNN=0.17361951).
• BP6: Variant 1-237657976-T-C is Benign according to our data. Variant chr1-237657976-T-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 43828.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=5, Likely_benign=6, Benign=1}. Variant chr1-237657976-T-C is described in Lovd as [Likely_benign].
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.000644 (98/152182) while in subpopulation NFE AF= 0.00131 (89/67972). AF 95% confidence interval is 0.00109. There are 0 homozygotes in gnomad4. There are 39 alleles in male gnomad4 subpopulation. This position pass quality control queck.
• BS2: High AC in GnomAd at 98 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RYR2	NM_001035.3	c.8162T>C	p.Ile2721Thr	missense_variant	54/105	ENST00000366574.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RYR2	ENST00000366574.7	c.8162T>C	p.Ile2721Thr	missense_variant	54/105	1	NM_001035.3	P1
RYR2	ENST00000660292.2	c.8162T>C	p.Ile2721Thr	missense_variant	54/106
RYR2	ENST00000659194.3	c.8162T>C	p.Ile2721Thr	missense_variant	54/105
RYR2	ENST00000609119.2	c.8162T>C	p.Ile2721Thr	missense_variant, NMD_transcript_variant	54/104	5

Frequencies

GnomAD3 genomes AF: 0.000644 AC: 98 AN: 152064 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.000193

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: 0.0000945

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00131

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000575 AC: 79 AN: 137332 Hom.: 0 AF XY: 0.000577 AC XY: 42 AN XY: 72842

Gnomad AFR exome AF: 0.000148

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: 0.000421

Gnomad NFE exome AF: 0.00124

Gnomad OTH exome AF: 0.000536

GnomAD4 exome AF: 0.00138 AC: 1881 AN: 1367528 Hom.: 6 Cov.: 26 AF XY: 0.00137 AC XY: 922 AN XY: 674114

Gnomad4 AFR exome AF: 0.000133

Gnomad4 AMR exome AF: 0.0000325

Gnomad4 ASJ exome AF: 0.0000405

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.000572

Gnomad4 NFE exome AF: 0.00170

Gnomad4 OTH exome AF: 0.000670

GnomAD4 genome AF: 0.000644 AC: 98 AN: 152182 Hom.: 0 Cov.: 33 AF XY: 0.000524 AC XY: 39 AN XY: 74400

Gnomad4 AFR AF: 0.000192

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.0000945

Gnomad4 NFE AF: 0.00131

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000975 Hom.: 0

Bravo AF: 0.000676

TwinsUK AF: 0.00270 AC: 10

ALSPAC AF: 0.00208 AC: 8

ESP6500AA AF: 0.000560 AC: 2

ESP6500EA AF: 0.000502 AC: 4

ExAC AF: 0.000244 AC: 25

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:6 Benign:12

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Benign:5

Likely benign, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -
Likely benign, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Likely benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Likely benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Likely benign, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -

not specified Uncertain:3 Benign:1

Uncertain significance, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Sep 21, 2012	The Ile2721Thr variant in RYR2 has not been reported in the literature nor previ ously identified by our laboratory. This variant has been identified in 4/7968 E uropean American chromosomes from a broad population by the NHLBI Exome Sequenci ng Project (http://evs.gs.washington.edu/EVS). Computational analyses (biochemic al amino acid properties, conservation, AlignGVGD, PolyPhen2, and SIFT) do not p rovide strong support for or against an impact to the protein. Additional inform ation is needed to fully assess the clinical significance of this variant. -
Uncertain significance, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Dec 01, 2016	- -
Likely benign, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Dec 29, 2020	Variant summary: RYR2 c.8162T>C (p.Ile2721Thr) results in a non-conservative amino acid change located in the Ryanodine receptor Ryr domain (IPR003032) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00057 in 137452 control chromosomes, predominantly at a frequency of 0.0012 within the Non-Finnish European subpopulation in the gnomAD database. The observed variant frequency within Non-Finnish European control individuals in the gnomAD database is approximately 20 fold of the estimated maximal expected allele frequency for a pathogenic variant in RYR2 causing Arrhythmia phenotype (6e-05), strongly suggesting that the variant is a benign polymorphism found primarily in populations of Non-Finnish European origin. c.8162T>C has been reported in the literature in individuals affected with Arrhythmia, LQTS, catecholaminergic polymorphic ventricular tachycardia, sudden arrhythmic death syndrome and Wolff-Parkinson-White syndrome (vanSpaendonck_2014, Hertz_2014, Landstrom_2017, Munroe_2018, Raju_2019, Coban-Akdemir_2020). These reports do not provide unequivocal conclusions about association of the variant with Arrhythmia. Co-occurrences with other pathogenic variants have been reported (TTN c.86171_86174dupAAAG, p.Asn28726Lysfs*3; LMNA c.725C>T, p.Ala242Val; KCNH2 c.1286del, p.A429Vfs*5), providing supporting evidence for a benign role. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. 11 ClinVar submitters (evaluation after 2014) cite the variant as uncertain significance (6x) and likely benign (5x). Based on the evidence outlined above, the variant was classified as likely benign. -
Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Sep 28, 2016	The I2721T variant of uncertain significance in the RYR2 gene has been previously reported intwo individuals (van Spaendonck-Zwarts et al., 2014; Hertz et al., 2015). This variant was initiallyreported as a variant of uncertain significance in one individual with atrial fibrillation and dilatedcardiomyopathy who was found to harbor additional variants of uncertain significance in theDMD and TTN genes (van Spaendonck-Zwarts et al., 2014). Subsequently, Hertz et al. (2015)reported I2721T in an individual diagnosed with Long QT syndrome at 19 years of age; however,she was also found to harbor a KCNH2 variant classified as likely pathogenic. This variant hasalso been identified independently and in conjunction with additional cardiogenetic variants inindividuals referred for arrhythmia and cardiomyopathy genetic testing at GeneDx; however, thusfar, segregation data is limited or absent for these individuals due to the lack of clinical informationprovided and/or insufficient participation by informative family members. Additionally, theI2721T variant is classified in ClinVar as a variant of uncertain significance by two clinicallaboratories (ClinVar SCV000060449.4; SCV000285751.1; Landrum et al., 2016). The I2721Tvariant was not observed with any significant frequency in approximately 5,800 individuals ofEuropean and African American ancestry in the NHLBI Exome Sequencing Project. Although thissubstitution occurs at a position where amino acids with similar properties to Isoleucine aretolerated across species, the I2721T variant is a non-conservative amino acid substitution, which islikely to impact secondary protein structure as these residues differ in polarity, charge, size and/orother properties. Consequently, in silico analysis predicts this variant is probably damaging to theprotein structure/function. Nevertheless, the I2721T variant is not located in one of the threehot-spot regions of the RYR2 gene, where the majority of pathogenic missense variants occur(Medeiros-Domingo et al., 2009).Therefore, based on the currently available information, it is unclear whether this variant ispathogenic or rare benign. -

Cardiomyopathy Benign:2

Likely benign, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Dec 20, 2018	Likely Benign variant based on current evidence: This missense variant is located in the cytoplasmic domain of the RYR2 protein. Computational prediction tools and conservation analyses suggest that this variant may have deleterious impact on the protein function. Computational splicing tools suggest that this variant may not impact RNA splicing. To our knowledge, functional assays have not been performed for this variant. This variant has been reported in an individual affected with long QT syndrome, who also carried a pathogenic truncation variant in the KCNH2 gene (PMID: 25467552). This variant has been identified in 97/163874 chromosomes (84/68536 non-Finnish European chromosomes, 0.1225%) in the general population by the Genome Aggregation Database (gnomAD). This variant allele frequency is greater than expected for the RYR2-related disorder based on prevalence, penetrance, and genetic heterogeneity. Based on available evidence, this variant is classified as Likely Benign. -
Likely benign, criteria provided, single submitter	clinical testing	CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario	Mar 24, 2020	- -

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). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Benign, criteria provided, single submitter	clinical testing	Invitae	Jan 28, 2024	- -

Wolff-Parkinson-White pattern Uncertain:1

Uncertain significance, no assertion criteria provided

research

Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine

Jul 14, 2017

This variant was identified in an individual with Wolff-Parkinson-White syndrome -

Arrhythmogenic right ventricular cardiomyopathy Uncertain:1

Uncertain significance, criteria provided, single submitter

research

CSER _CC_NCGL, University of Washington

Oct 01, 2016

Found in patient having exome sequencing for an unrelated indication. No known history of arrhythmogenic right ventricular dysplasia. This interpretation considers GERP score and allele frequency data, in addition to published reports of the variant in the literature, available at the time of review. -

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). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -

RYR2-related disorder Benign:1

Likely benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Jan 31, 2022

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Cardiovascular phenotype Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Ambry Genetics

Jul 20, 2023

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.38
BayesDel_addAF	Benign	-0.10	T
BayesDel_noAF	Uncertain	0.070
Cadd	Uncertain	24
Dann	Uncertain	1.0
DEOGEN2	Pathogenic	0.83	D;T
Eigen	Uncertain	0.43
Eigen_PC	Uncertain	0.52
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Uncertain	0.91	D;D
M_CAP	Uncertain	0.19	D
MetaRNN	Benign	0.17	T;T
MetaSVM	Uncertain	0.50	D
MutationAssessor	Benign	0.84	L;.
MutationTaster	Benign	1.0	D
PrimateAI	Uncertain	0.78	T
PROVEAN	Uncertain	-3.6	D;.
REVEL	Uncertain	0.59
Sift	Benign	0.17	T;.
Polyphen		0.85	P;.
Vest4		0.65
MVP		0.78
MPC		1.2
ClinPred		0.10	T
GERP RS		6.2
Varity_R		0.28
gMVP		0.43

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: rs201500134; hg19: chr1-237821276;