1-237042458-G-GGCC
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_001035.3(RYR2):c.-50_-48dup variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00026 in 1,228,100 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0012 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00013 ( 0 hom. )
Consequence
RYR2
NM_001035.3 5_prime_UTR
NM_001035.3 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.215
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 -10 ACMG points.
BP6
?
Variant 1-237042458-G-GGCC is Benign according to our data. Variant chr1-237042458-G-GGCC is described in ClinVar as [Benign]. Clinvar id is 201174.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00116 (176/151914) while in subpopulation AFR AF= 0.00354 (147/41536). AF 95% confidence interval is 0.00307. There are 0 homozygotes in gnomad4. There are 89 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
High AC in GnomAd at 176 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RYR2 | NM_001035.3 | c.-50_-48dup | 5_prime_UTR_variant | 1/105 | ENST00000366574.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RYR2 | ENST00000366574.7 | c.-50_-48dup | 5_prime_UTR_variant | 1/105 | 1 | NM_001035.3 | P1 | ||
RYR2 | ENST00000659194.3 | c.-50_-48dup | 5_prime_UTR_variant | 1/105 | |||||
RYR2 | ENST00000660292.2 | c.-50_-48dup | 5_prime_UTR_variant | 1/106 | |||||
RYR2 | ENST00000609119.2 | c.-50_-48dup | 5_prime_UTR_variant, NMD_transcript_variant | 1/104 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00116 AC: 176AN: 151806Hom.: 0 Cov.: 33
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GnomAD4 exome AF: 0.000133 AC: 143AN: 1076186Hom.: 0 Cov.: 25 AF XY: 0.000157 AC XY: 80AN XY: 508380
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GnomAD4 genome ? AF: 0.00116 AC: 176AN: 151914Hom.: 0 Cov.: 33 AF XY: 0.00120 AC XY: 89AN XY: 74266
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 25, 2014 | The variant is found in CARDIOMYOPATHY panel(s). - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at