chr19-38433746-G-GC
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_000540.3(RYR1):c.-81dup variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000021 ( 0 hom., cov: 30)
Exomes 𝑓: 0.0031 ( 2 hom. )
Failed GnomAD Quality Control
Consequence
RYR1
NM_000540.3 5_prime_UTR
NM_000540.3 5_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.43
Genes affected
RYR1 (HGNC:10483): (ryanodine receptor 1) This gene encodes a ryanodine receptor found in skeletal muscle. The encoded protein functions as a calcium release channel in the sarcoplasmic reticulum but also serves to connect the sarcoplasmic reticulum and transverse tubule. Mutations in this gene are associated with malignant hyperthermia susceptibility, central core disease, and minicore myopathy with external ophthalmoplegia. Alternatively spliced transcripts encoding different isoforms have been described. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RYR1 | NM_000540.3 | c.-81dup | 5_prime_UTR_variant | 1/106 | ENST00000359596.8 | NP_000531.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RYR1 | ENST00000359596.8 | c.-81dup | 5_prime_UTR_variant | 1/106 | 5 | NM_000540.3 | ENSP00000352608 | A2 | ||
RYR1 | ENST00000355481.8 | c.-81dup | 5_prime_UTR_variant | 1/105 | 1 | ENSP00000347667 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 3AN: 145246Hom.: 0 Cov.: 30 FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00308 AC: 1155AN: 374914Hom.: 2 Cov.: 0 AF XY: 0.00286 AC XY: 598AN XY: 208814
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Data not reliable, filtered out with message: AS_VQSR
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000207 AC: 3AN: 145246Hom.: 0 Cov.: 30 AF XY: 0.0000141 AC XY: 1AN XY: 70886
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:4
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Central core myopathy Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Malignant hyperthermia of anesthesia Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Multiminicore myopathy Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Neuromuscular disease, congenital, with uniform type 1 fiber Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at