rs779631412
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_001035.3(RYR2):c.309+9_309+13del variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000223 in 1,522,492 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000023 ( 0 hom. )
Consequence
RYR2
NM_001035.3 splice_region, intron
NM_001035.3 splice_region, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.979
Genes affected
RYR2 (HGNC:10484): (ryanodine receptor 2) This gene encodes a ryanodine receptor found in cardiac muscle sarcoplasmic reticulum. The encoded protein is one of the components of a calcium channel, composed of a tetramer of the ryanodine receptor proteins and a tetramer of FK506 binding protein 1B proteins, that supplies calcium to cardiac muscle. Mutations in this gene are associated with stress-induced polymorphic ventricular tachycardia and arrhythmogenic right ventricular dysplasia. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP6
?
Variant 1-237364379-CATCTT-C is Benign according to our data. Variant chr1-237364379-CATCTT-C is described in ClinVar as [Likely_benign]. Clinvar id is 412825.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAdExome4 at 31 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RYR2 | NM_001035.3 | c.309+9_309+13del | splice_region_variant, intron_variant | ENST00000366574.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RYR2 | ENST00000366574.7 | c.309+9_309+13del | splice_region_variant, intron_variant | 1 | NM_001035.3 | P1 | |||
RYR2 | ENST00000659194.3 | c.309+9_309+13del | splice_region_variant, intron_variant | ||||||
RYR2 | ENST00000660292.2 | c.309+9_309+13del | splice_region_variant, intron_variant | ||||||
RYR2 | ENST00000609119.2 | c.309+9_309+13del | splice_region_variant, intron_variant, NMD_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000198 AC: 3AN: 151374Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000640 AC: 13AN: 203094Hom.: 0 AF XY: 0.0000548 AC XY: 6AN XY: 109520
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GnomAD4 exome AF: 0.0000226 AC: 31AN: 1371016Hom.: 0 AF XY: 0.0000264 AC XY: 18AN XY: 682752
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GnomAD4 genome ? AF: 0.0000198 AC: 3AN: 151476Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 73996
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Catecholaminergic polymorphic ventricular tachycardia 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 08, 2023 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at