rs80354707
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The ENST00000634891.2(RYR3):c.5620-5C>G variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0012 in 1,613,538 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
ENST00000634891.2 splice_region, splice_polypyrimidine_tract, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RYR3 | NM_001036.6 | c.5620-5C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000634891.2 | NP_001027.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RYR3 | ENST00000634891.2 | c.5620-5C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001036.6 | ENSP00000489262 | P4 | |||
RYR3 | ENST00000389232.9 | c.5620-5C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | ENSP00000373884 | A1 | ||||
RYR3 | ENST00000415757.7 | c.5620-5C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 2 | ENSP00000399610 | A2 | ||||
RYR3 | ENST00000634418.1 | c.5620-5C>G | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 5 | ENSP00000489529 |
Frequencies
GnomAD3 genomes AF: 0.00665 AC: 1012AN: 152150Hom.: 8 Cov.: 31
GnomAD3 exomes AF: 0.00153 AC: 381AN: 249220Hom.: 4 AF XY: 0.00116 AC XY: 157AN XY: 135212
GnomAD4 exome AF: 0.000628 AC: 917AN: 1461272Hom.: 15 Cov.: 30 AF XY: 0.000531 AC XY: 386AN XY: 726934
GnomAD4 genome AF: 0.00669 AC: 1019AN: 152266Hom.: 9 Cov.: 31 AF XY: 0.00653 AC XY: 486AN XY: 74468
ClinVar
Submissions by phenotype
Epileptic encephalopathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 17, 2024 | - - |
RYR3-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Apr 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