rs35018208
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP6
The NM_000540.3(RYR1):c.631+39del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000019 in 1,475,014 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in Lovd as Benign (no stars).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 0)
Exomes 𝑓: 0.000020 ( 0 hom. )
Consequence
RYR1
NM_000540.3 intron
NM_000540.3 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.767
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 Likely_benign. Variant got -1 ACMG points.
BP6
?
Variant 19-38444710-TC-T is Benign according to our data. Variant chr19-38444710-TC-T is described in Lovd as [Benign].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RYR1 | NM_000540.3 | c.631+39del | intron_variant | ENST00000359596.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RYR1 | ENST00000359596.8 | c.631+39del | intron_variant | 5 | NM_000540.3 | A2 | |||
RYR1 | ENST00000355481.8 | c.631+39del | intron_variant | 1 | P4 | ||||
RYR1 | ENST00000599547.6 | c.631+39del | intron_variant, NMD_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000135 AC: 2AN: 148680Hom.: 0 Cov.: 0
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GnomAD3 exomes AF: 0.0000751 AC: 16AN: 213030Hom.: 0 AF XY: 0.0000868 AC XY: 10AN XY: 115266
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GnomAD4 exome AF: 0.0000196 AC: 26AN: 1326218Hom.: 0 Cov.: 21 AF XY: 0.0000241 AC XY: 16AN XY: 664104
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GnomAD4 genome ? AF: 0.0000134 AC: 2AN: 148796Hom.: 0 Cov.: 0 AF XY: 0.0000138 AC XY: 1AN XY: 72350
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at