rs41279216
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001036.6(RYR3):c.8136+9C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00403 in 1,613,344 control chromosomes in the GnomAD database, including 245 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.022 ( 126 hom., cov: 32)
Exomes 𝑓: 0.0022 ( 119 hom. )
Consequence
RYR3
NM_001036.6 intron
NM_001036.6 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.15
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
?
Variant 15-33748269-C-G is Benign according to our data. Variant chr15-33748269-C-G is described in ClinVar as [Benign]. Clinvar id is 461965.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0743 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RYR3 | NM_001036.6 | c.8136+9C>G | intron_variant | ENST00000634891.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RYR3 | ENST00000634891.2 | c.8136+9C>G | intron_variant | 1 | NM_001036.6 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0220 AC: 3340AN: 152162Hom.: 128 Cov.: 32
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GnomAD3 exomes AF: 0.00577 AC: 1429AN: 247760Hom.: 48 AF XY: 0.00437 AC XY: 588AN XY: 134476
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GnomAD4 exome AF: 0.00216 AC: 3162AN: 1461064Hom.: 119 Cov.: 31 AF XY: 0.00183 AC XY: 1329AN XY: 726786
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GnomAD4 genome ? AF: 0.0220 AC: 3347AN: 152280Hom.: 126 Cov.: 32 AF XY: 0.0211 AC XY: 1573AN XY: 74448
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Epileptic encephalopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 15, 2024 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 10, 2019 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at