rs16835325

Variant names:

• chr1-237496006-C-T
• rs16835325
• NM_001035.3:c.1962-505C>T

Variant summary

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

The NM_001035.3(RYR2):​c.1962-505C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0773 in 152,194 control chromosomes in the GnomAD database, including 1,371 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 0.077 (1371 hom., cov: 32)
• Consequence: RYR2 NM_001035.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.71

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RYR2	NM_001035.3	c.1962-505C>T		intron_variant	Intron 19 of 104	ENST00000366574.7	NP_001026.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RYR2	ENST00000366574.7	c.1962-505C>T		intron_variant	Intron 19 of 104	1	NM_001035.3	ENSP00000355533.2
RYR2	ENST00000609119.2	n.1962-505C>T		intron_variant	Intron 19 of 103	5		ENSP00000499659.2
RYR2	ENST00000660292.2	c.1962-505C>T		intron_variant	Intron 19 of 105			ENSP00000499787.2
RYR2	ENST00000659194.3	c.1962-505C>T		intron_variant	Intron 19 of 104			ENSP00000499653.3

Frequencies

GnomAD3 genomes AF: 0.0771 AC: 11730 AN: 152076 Hom.: 1365 Cov.: 32

Gnomad AFR AF: 0.251

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0365

Gnomad ASJ AF: 0.00836

Gnomad EAS AF: 0.0287

Gnomad SAS AF: 0.0166

Gnomad FIN AF: 0.00254

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.00517

Gnomad OTH AF: 0.0684

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

GnomAD4 genome AF: 0.0773 AC: 11757 AN: 152194 Hom.: 1371 Cov.: 32 AF XY: 0.0748 AC XY: 5562 AN XY: 74404

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.0363

Gnomad4 ASJ AF: 0.00836

Gnomad4 EAS AF: 0.0285

Gnomad4 SAS AF: 0.0162

Gnomad4 FIN AF: 0.00254

Gnomad4 NFE AF: 0.00518

Gnomad4 OTH AF: 0.0681

Alfa AF: 0.0199 Hom.: 223

Bravo AF: 0.0876

Asia WGS AF: 0.0430 AC: 148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.16
DANN	Benign	0.27

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: rs16835325; hg19: chr1-237659306;