rs553354987

Variant names:

• chr15-33660284-A-C
• NM_001036.6:c.4483A>C

Your query was ambiguous. Multiple possible variants found:

• chr15-33660284-A-C
• chr15-33660284-A-G
• chr15-33660284-A-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001036.6(RYR3):​c.4483A>C​(p.Ile1495Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000142 in 1,410,894 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: RYR3 NM_001036.6 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.90

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 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.23567164).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RYR3	NM_001036.6	c.4483A>C	p.Ile1495Leu	missense_variant	Exon 34 of 104	ENST00000634891.2	NP_001027.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RYR3	ENST00000634891.2	c.4483A>C	p.Ile1495Leu	missense_variant	Exon 34 of 104	1	NM_001036.6	ENSP00000489262.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000142 AC: 2 AN: 1410894 Hom.: 0 Cov.: 32 AF XY: 0.00000143 AC XY: 1 AN XY: 696900

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000184

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.079
BayesDel_addAF	Pathogenic	0.19	D
BayesDel_noAF	Uncertain	0.040
CADD	Benign	19
DANN	Benign	0.82
DEOGEN2	Benign	0.26	T;.;.;.;.
Eigen	Benign	-0.45
Eigen_PC	Benign	-0.17
FATHMM_MKL	Uncertain	0.94	D
LIST_S2	Benign	0.84	T;T;T;T;T
M_CAP	Benign	0.045	D
MetaRNN	Benign	0.24	T;T;T;T;T
MetaSVM	Uncertain	-0.22	T
MutationAssessor	Benign	-0.35	N;N;.;.;.
PrimateAI	Uncertain	0.61	T
PROVEAN	Benign	0.36	.;N;N;.;.
REVEL	Uncertain	0.48
Sift	Benign	1.0	.;T;T;.;.
Polyphen		0.017	B;B;.;.;.
Vest4		0.47
MutPred		0.42		Loss of catalytic residue at P1497 (P = 0.0333);Loss of catalytic residue at P1497 (P = 0.0333);Loss of catalytic residue at P1497 (P = 0.0333);Loss of catalytic residue at P1497 (P = 0.0333);Loss of catalytic residue at P1497 (P = 0.0333);
MVP		0.69
MPC		0.18
ClinPred		0.76	D
GERP RS		4.8
Varity_R		0.19
gMVP		0.47

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr15-33952485;