rs2177065

chr1-237751707-A-Gchr1-237751707-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001035.3(RYR2):c.11146-4581A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.871 in 152,198 control chromosomes in the GnomAD database, including 59,783 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 0.87 (59783 hom., cov: 32)
• Consequence: RYR2 NM_001035.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RYR2	NM_001035.3	c.11146-4581A>G		intron_variant		ENST00000366574.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RYR2	ENST00000366574.7	c.11146-4581A>G		intron_variant		1	NM_001035.3	P1
RYR2	ENST00000659194.3	c.11134-4581A>G		intron_variant
RYR2	ENST00000660292.2	c.11134-4581A>G		intron_variant
RYR2	ENST00000609119.2	c.*2181-3354A>G		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.871 AC: 132474 AN: 152080 Hom.: 59776 Cov.: 32

Gnomad AFR AF: 0.606

Gnomad AMI AF: 0.927

Gnomad AMR AF: 0.921

Gnomad ASJ AF: 0.989

Gnomad EAS AF: 0.941

Gnomad SAS AF: 0.978

Gnomad FIN AF: 0.984

Gnomad MID AF: 0.971

Gnomad NFE AF: 0.982

Gnomad OTH AF: 0.894

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

GnomAD4 genome AF: 0.871 AC: 132521 AN: 152198 Hom.: 59783 Cov.: 32 AF XY: 0.875 AC XY: 65134 AN XY: 74420

Gnomad4 AFR AF: 0.606

Gnomad4 AMR AF: 0.920

Gnomad4 ASJ AF: 0.989

Gnomad4 EAS AF: 0.941

Gnomad4 SAS AF: 0.979

Gnomad4 FIN AF: 0.984

Gnomad4 NFE AF: 0.982

Gnomad4 OTH AF: 0.895

Alfa AF: 0.961 Hom.: 39561

Bravo AF: 0.854

Asia WGS AF: 0.937 AC: 3247 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.52
Dann	Benign	0.57

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: rs2177065; hg19: chr1-237915007;