rs531243171
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_000540.3(RYR1):c.4764G>A(p.Pro1588=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000199 in 1,561,014 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. P1588P) 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 -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RYR1 | NM_000540.3 | c.4764G>A | p.Pro1588= | synonymous_variant | 33/106 | ENST00000359596.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RYR1 | ENST00000359596.8 | c.4764G>A | p.Pro1588= | synonymous_variant | 33/106 | 5 | NM_000540.3 | A2 | |
RYR1 | ENST00000355481.8 | c.4764G>A | p.Pro1588= | synonymous_variant | 33/105 | 1 | P4 | ||
RYR1 | ENST00000599547.6 | c.4764G>A | p.Pro1588= | synonymous_variant, NMD_transcript_variant | 33/80 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152168Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000480 AC: 81AN: 168594Hom.: 1 AF XY: 0.000727 AC XY: 65AN XY: 89464
GnomAD4 exome AF: 0.000209 AC: 295AN: 1408728Hom.: 6 Cov.: 32 AF XY: 0.000328 AC XY: 228AN XY: 695808
GnomAD4 genome AF: 0.000105 AC: 16AN: 152286Hom.: 0 Cov.: 31 AF XY: 0.000161 AC XY: 12AN XY: 74464
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Malignant hyperthermia, susceptibility to, 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | All of Us Research Program, National Institutes of Health | Jan 03, 2024 | - - |
RYR1-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 27, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at