rs765250427
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4BP6_ModerateBP7
The NM_000540.3(RYR1):c.9679C>A(p.Arg3227=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000568 in 1,585,682 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 (★). Synonymous variant affecting the same amino acid position (i.e. R3227R) has been classified as Likely benign.
Frequency
Consequence
NM_000540.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RYR1 | NM_000540.3 | c.9679C>A | p.Arg3227= | synonymous_variant | 65/106 | ENST00000359596.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RYR1 | ENST00000359596.8 | c.9679C>A | p.Arg3227= | synonymous_variant | 65/106 | 5 | NM_000540.3 | A2 | |
RYR1 | ENST00000355481.8 | c.9679C>A | p.Arg3227= | synonymous_variant | 65/105 | 1 | P4 | ||
RYR1 | ENST00000594335.5 | c.*422C>A | 3_prime_UTR_variant, NMD_transcript_variant | 25/49 | 1 | ||||
RYR1 | ENST00000599547.6 | c.*438C>A | 3_prime_UTR_variant, NMD_transcript_variant | 64/80 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152206Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000345 AC: 7AN: 202726Hom.: 0 AF XY: 0.00000912 AC XY: 1AN XY: 109640
GnomAD4 exome AF: 0.00000558 AC: 8AN: 1433476Hom.: 0 Cov.: 31 AF XY: 0.00000282 AC XY: 2AN XY: 710254
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152206Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74366
ClinVar
Submissions by phenotype
RYR1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 14, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at