15-33639030-T-C

Position:

• chr15-33639030-T-C

Variant summary

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

The ENST00000634891.2(RYR3):​c.3556+2480T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.193 in 152,098 control chromosomes in the GnomAD database, including 3,332 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 0.19 (3332 hom., cov: 32)
• Consequence: RYR3 ENST00000634891.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.470

Genes affected

RYR3 (HGNC:10485): (ryanodine receptor 3) The protein encoded by this gene is a ryanodine receptor, which functions to release calcium from intracellular storage for use in many cellular processes. For example, the encoded protein is involved in skeletal muscle contraction by releasing calcium from the sarcoplasmic reticulum followed by depolarization of T-tubules. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RYR3	NM_001036.6	c.3556+2480T>C		intron_variant		ENST00000634891.2	NP_001027.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RYR3	ENST00000634891.2	c.3556+2480T>C		intron_variant		1	NM_001036.6	ENSP00000489262	P4
RYR3	ENST00000389232.9	c.3556+2480T>C		intron_variant		5		ENSP00000373884	A1
RYR3	ENST00000415757.7	c.3556+2480T>C		intron_variant		2		ENSP00000399610	A2
RYR3	ENST00000634418.1	c.3556+2480T>C		intron_variant		5		ENSP00000489529

Frequencies

GnomAD3 genomes AF: 0.193 AC: 29388 AN: 151978 Hom.: 3320 Cov.: 32

Gnomad AFR AF: 0.267

Gnomad AMI AF: 0.0868

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.487

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.183

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

GnomAD4 genome AF: 0.193 AC: 29423 AN: 152098 Hom.: 3332 Cov.: 32 AF XY: 0.197 AC XY: 14685 AN XY: 74368

Gnomad4 AFR AF: 0.267

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.145

Gnomad4 EAS AF: 0.486

Gnomad4 SAS AF: 0.210

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.187

Alfa AF: 0.170 Hom.: 512

Bravo AF: 0.194

Asia WGS AF: 0.342 AC: 1186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.93
DANN	Benign	0.48

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: rs10851886; hg19: chr15-33931231;