rs10925416

chr1-237439366-C-T

Variant summary

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

The NM_001035.3(RYR2):c.1006-1953C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.151 in 152,086 control chromosomes in the GnomAD database, including 1,884 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 0.15 (1884 hom., cov: 33)
• Consequence: RYR2 NM_001035.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662

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=-1.0).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RYR2	NM_001035.3	c.1006-1953C>T		intron_variant		ENST00000366574.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RYR2	ENST00000366574.7	c.1006-1953C>T		intron_variant		1	NM_001035.3	P1
RYR2	ENST00000659194.3	c.1006-1953C>T		intron_variant
RYR2	ENST00000660292.2	c.1006-1953C>T		intron_variant
RYR2	ENST00000609119.2	c.1006-1953C>T		intron_variant, NMD_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.151 AC: 22928 AN: 151968 Hom.: 1883 Cov.: 33

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.0967

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.0807

Gnomad EAS AF: 0.185

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.151 AC: 22964 AN: 152086 Hom.: 1884 Cov.: 33 AF XY: 0.153 AC XY: 11409 AN XY: 74352

Gnomad4 AFR AF: 0.170

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.0807

Gnomad4 EAS AF: 0.184

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.155

Alfa AF: 0.130 Hom.: 2590

Bravo AF: 0.162

Asia WGS AF: 0.185 AC: 640 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.80
Dann	Benign	0.49

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: rs10925416; hg19: chr1-237602666;