19-38483460-C-G
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_ModerateBP6_Very_StrongBP7
The NM_000540.3(RYR1):āc.4878C>Gā(p.Ala1626=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000523 in 1,568,394 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. A1626A) has been classified as Likely benign.
Frequency
Consequence
NM_000540.3 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RYR1 | NM_000540.3 | c.4878C>G | p.Ala1626= | synonymous_variant | 33/106 | ENST00000359596.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RYR1 | ENST00000359596.8 | c.4878C>G | p.Ala1626= | synonymous_variant | 33/106 | 5 | NM_000540.3 | A2 | |
RYR1 | ENST00000355481.8 | c.4878C>G | p.Ala1626= | synonymous_variant | 33/105 | 1 | P4 | ||
RYR1 | ENST00000599547.6 | c.4878C>G | p.Ala1626= | synonymous_variant, NMD_transcript_variant | 33/80 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000217 AC: 33AN: 152102Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000341 AC: 6AN: 175698Hom.: 0 AF XY: 0.0000105 AC XY: 1AN XY: 95072
GnomAD4 exome AF: 0.0000346 AC: 49AN: 1416174Hom.: 0 Cov.: 32 AF XY: 0.0000257 AC XY: 18AN XY: 700894
GnomAD4 genome AF: 0.000217 AC: 33AN: 152220Hom.: 0 Cov.: 31 AF XY: 0.000215 AC XY: 16AN XY: 74434
ClinVar
Submissions by phenotype
RYR1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 03, 2024 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at