rs16972317

Positions:

• chr15-33562974-C-A
• chr15-33562974-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001036.6(RYR3):​c.1110C>A​(p.Asp370Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: RYR3 NM_001036.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.77

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 Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RYR3	NM_001036.6	c.1110C>A	p.Asp370Glu	missense_variant	11/104	ENST00000634891.2	NP_001027.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RYR3	ENST00000634891.2	c.1110C>A	p.Asp370Glu	missense_variant	11/104	1	NM_001036.6	ENSP00000489262	P4
RYR3	ENST00000389232.9	c.1110C>A	p.Asp370Glu	missense_variant	11/104	5		ENSP00000373884	A1
RYR3	ENST00000415757.7	c.1110C>A	p.Asp370Glu	missense_variant	11/103	2		ENSP00000399610	A2
RYR3	ENST00000634418.1	c.1110C>A	p.Asp370Glu	missense_variant	11/102	5		ENSP00000489529

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.37
BayesDel_addAF	Uncertain	0.076	D
BayesDel_noAF	Benign	-0.13
CADD	Benign	15
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.57	D;.;.;.;.
Eigen	Benign	-0.25
Eigen_PC	Benign	-0.22
FATHMM_MKL	Uncertain	0.83	D
LIST_S2	Uncertain	0.91	D;D;D;D;D
M_CAP	Benign	0.066	D
MetaRNN	Uncertain	0.66	D;D;D;D;D
MetaSVM	Benign	-0.32	T
MutationAssessor	Benign	1.3	L;L;.;.;.
MutationTaster	Benign	1.0	D;D
PrimateAI	Uncertain	0.65	T
PROVEAN	Uncertain	-3.0	.;D;D;.;.
REVEL	Uncertain	0.56
Sift	Benign	1.0	.;T;T;.;.
Polyphen		0.65	P;D;.;.;.
Vest4		0.64
MutPred		0.43		Gain of methylation at K372 (P = 0.1018);Gain of methylation at K372 (P = 0.1018);Gain of methylation at K372 (P = 0.1018);Gain of methylation at K372 (P = 0.1018);Gain of methylation at K372 (P = 0.1018);
MVP		0.84
MPC		0.67
ClinPred		0.99	D
GERP RS		0.35
Varity_R		0.25
gMVP		0.19

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: rs16972317; hg19: chr15-33855175; COSMIC: COSV66803350;