rs12136903

Variant names:

• chr1-237803577-A-G
• rs12136903
• NM_001035.3:c.14151+1661A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001035.3(RYR2):​c.14151+1661A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0461 in 152,046 control chromosomes in the GnomAD database, including 214 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.046 (214 hom., cov: 32)
• Consequence: RYR2 NM_001035.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.15
• Publications: 1 publications found

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]

RYR2 Gene-Disease associations (from GenCC):

• arrhythmogenic right ventricular dysplasia 2

  Inheritance: AD Classification: DEFINITIVE, NO_KNOWN Submitted by: Laboratory for Molecular Medicine, Ambry Genetics
• catecholaminergic polymorphic ventricular tachycardia

  Inheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, ClinGen, G2P
• catecholaminergic polymorphic ventricular tachycardia 1

  Inheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae)
• hypertrophic cardiomyopathy

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen
• arrhythmogenic right ventricular cardiomyopathy

  Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.061 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RYR2	NM_001035.3	c.14151+1661A>G		intron_variant	Intron 98 of 104	ENST00000366574.7	NP_001026.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RYR2	ENST00000366574.7	c.14151+1661A>G		intron_variant	Intron 98 of 104	1	NM_001035.3	ENSP00000355533.2
RYR2	ENST00000661330.2	c.14169+1661A>G		intron_variant	Intron 99 of 105			ENSP00000499393.2
RYR2	ENST00000609119.2	n.*5243+1661A>G		intron_variant	Intron 97 of 103	5		ENSP00000499659.2

Frequencies

GnomAD3 genomes AF: 0.0461 AC: 7002 AN: 151928 Hom.: 214 Cov.: 32

Gnomad AFR AF: 0.0206

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.0373

Gnomad ASJ AF: 0.0266

Gnomad EAS AF: 0.00483

Gnomad SAS AF: 0.0160

Gnomad FIN AF: 0.0897

Gnomad MID AF: 0.00962

Gnomad NFE AF: 0.0626

Gnomad OTH AF: 0.0421

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0461 AC: 7003 AN: 152046 Hom.: 214 Cov.: 32 AF XY: 0.0463 AC XY: 3444 AN XY: 74320

African (AFR) AF: 0.0206 AC: 854 AN: 41478

American (AMR) AF: 0.0372 AC: 567 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0266 AC: 92 AN: 3464

East Asian (EAS) AF: 0.00484 AC: 25 AN: 5164

South Asian (SAS) AF: 0.0162 AC: 78 AN: 4810

European-Finnish (FIN) AF: 0.0897 AC: 949 AN: 10582

Middle Eastern (MID) AF: 0.00690 AC: 2 AN: 290

European-Non Finnish (NFE) AF: 0.0626 AC: 4254 AN: 67980

Other (OTH) AF: 0.0417 AC: 88 AN: 2110

Alfa AF: 0.0589 Hom.: 34

Bravo AF: 0.0407

Asia WGS AF: 0.0180 AC: 64 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.12
DANN	Benign	0.50
PhyloP100		-3.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12136903; hg19: chr1-237966877;