rs1465698
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_000540.3(RYR1):āc.7584C>Gā(p.Pro2528=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000546 in 1,613,010 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. P2528P) has been classified as Likely benign.
Frequency
Consequence
NM_000540.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RYR1 | NM_000540.3 | c.7584C>G | p.Pro2528= | synonymous_variant | 47/106 | ENST00000359596.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RYR1 | ENST00000359596.8 | c.7584C>G | p.Pro2528= | synonymous_variant | 47/106 | 5 | NM_000540.3 | A2 | |
RYR1 | ENST00000355481.8 | c.7584C>G | p.Pro2528= | synonymous_variant | 47/105 | 1 | P4 | ||
RYR1 | ENST00000594335.5 | c.1038C>G | p.Pro346= | synonymous_variant, NMD_transcript_variant | 8/49 | 1 | |||
RYR1 | ENST00000599547.6 | c.7584C>G | p.Pro2528= | synonymous_variant, NMD_transcript_variant | 47/80 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000309 AC: 47AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000895 AC: 22AN: 245820Hom.: 0 AF XY: 0.0000674 AC XY: 9AN XY: 133458
GnomAD4 exome AF: 0.0000281 AC: 41AN: 1460874Hom.: 0 Cov.: 41 AF XY: 0.0000261 AC XY: 19AN XY: 726708
GnomAD4 genome AF: 0.000309 AC: 47AN: 152136Hom.: 0 Cov.: 32 AF XY: 0.000377 AC XY: 28AN XY: 74326
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Aug 10, 2018 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2022 | RYR1: BP4, BP7 - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 29, 2018 | - - |
RYR1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 15, 2024 | - - |
Congenital myopathy with fiber type disproportion;C0751951:Central core myopathy;C1840365:King Denborough syndrome;C1850674:Congenital multicore myopathy with external ophthalmoplegia;C2930980:Malignant hyperthermia, susceptibility to, 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Jul 27, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at