rs2291734
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001036.6(RYR3):c.3382-77G>A 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 1,266,648 control chromosomes in the GnomAD database, including 25,325 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 0.16 ( 2279 hom., cov: 32)
Exomes 𝑓: 0.20 ( 23046 hom. )
Consequence
RYR3
NM_001036.6 intron
NM_001036.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.711
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RYR3 | NM_001036.6 | c.3382-77G>A | intron_variant | ENST00000634891.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RYR3 | ENST00000634891.2 | c.3382-77G>A | intron_variant | 1 | NM_001036.6 | P4 | |||
RYR3 | ENST00000389232.9 | c.3382-77G>A | intron_variant | 5 | A1 | ||||
RYR3 | ENST00000415757.7 | c.3382-77G>A | intron_variant | 2 | A2 | ||||
RYR3 | ENST00000634418.1 | c.3382-77G>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.156 AC: 23627AN: 151890Hom.: 2274 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
23627
AN:
151890
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.198 AC: 220512AN: 1114640Hom.: 23046 AF XY: 0.199 AC XY: 113152AN XY: 569870
GnomAD4 exome
AF:
AC:
220512
AN:
1114640
Hom.:
AF XY:
AC XY:
113152
AN XY:
569870
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.156 AC: 23652AN: 152008Hom.: 2279 Cov.: 32 AF XY: 0.159 AC XY: 11847AN XY: 74300
GnomAD4 genome
?
AF:
AC:
23652
AN:
152008
Hom.:
Cov.:
32
AF XY:
AC XY:
11847
AN XY:
74300
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
697
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at