rs35563566
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2
The NM_001035.3(RYR2):c.14091-12_14091-11del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00116 in 1,354,864 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in Lovd as Benign (no stars).
Frequency
Genomes: 𝑓 0.0000067 ( 0 hom., cov: 0)
Exomes 𝑓: 0.0013 ( 0 hom. )
Consequence
RYR2
NM_001035.3 intron
NM_001035.3 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.362
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 Benign. Variant got -9 ACMG points.
BP6
?
Variant 1-237801833-ATT-A is Benign according to our data. Variant chr1-237801833-ATT-A is described in Lovd as [Benign].
BS1
?
Variant frequency is greater than expected in population amr. gnomad4_exome allele frequency = 0.00131 (1575/1206654) while in subpopulation AMR AF= 0.00222 (85/38332). AF 95% confidence interval is 0.00184. There are 0 homozygotes in gnomad4_exome. There are 832 alleles in male gnomad4_exome subpopulation. This position pass quality control queck.
BS2
?
High AC in GnomAdExome4 at 1575 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RYR2 | NM_001035.3 | c.14091-12_14091-11del | intron_variant | ENST00000366574.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RYR2 | ENST00000366574.7 | c.14091-12_14091-11del | intron_variant | 1 | NM_001035.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000675 AC: 1AN: 148140Hom.: 0 Cov.: 0
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GnomAD4 exome AF: 0.00131 AC: 1575AN: 1206654Hom.: 0 AF XY: 0.00138 AC XY: 832AN XY: 602628
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GnomAD4 genome ? AF: 0.00000675 AC: 1AN: 148210Hom.: 0 Cov.: 0 AF XY: 0.0000139 AC XY: 1AN XY: 72162
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ClinVar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at