15-33726433-G-C
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001036.6(RYR3):āc.6960G>Cā(p.Leu2320=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00044 in 1,611,974 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ). Synonymous variant affecting the same amino acid position (i.e. L2320L) has been classified as Likely benign.
Frequency
Consequence
NM_001036.6 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RYR3 | NM_001036.6 | c.6960G>C | p.Leu2320= | synonymous_variant | 46/104 | ENST00000634891.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RYR3 | ENST00000634891.2 | c.6960G>C | p.Leu2320= | synonymous_variant | 46/104 | 1 | NM_001036.6 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000703 AC: 107AN: 152198Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00154 AC: 377AN: 244868Hom.: 4 AF XY: 0.00159 AC XY: 211AN XY: 132624
GnomAD4 exome AF: 0.000412 AC: 602AN: 1459658Hom.: 6 Cov.: 31 AF XY: 0.000460 AC XY: 334AN XY: 725784
GnomAD4 genome AF: 0.000709 AC: 108AN: 152316Hom.: 2 Cov.: 32 AF XY: 0.000779 AC XY: 58AN XY: 74486
ClinVar
Submissions by phenotype
Epileptic encephalopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 15, 2022 | - - |
RYR3-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 17, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at