rs1258139963
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_001035.3(RYR2):c.11622T>C(p.Thr3874=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000072 in 1,388,570 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. T3874T) has been classified as Likely benign.
Frequency
Consequence
NM_001035.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RYR2 | NM_001035.3 | c.11622T>C | p.Thr3874= | synonymous_variant | 86/105 | ENST00000366574.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RYR2 | ENST00000366574.7 | c.11622T>C | p.Thr3874= | synonymous_variant | 86/105 | 1 | NM_001035.3 | P1 | |
RYR2 | ENST00000660292.2 | c.11643T>C | p.Thr3881= | synonymous_variant | 87/106 | ||||
RYR2 | ENST00000659194.3 | c.11610T>C | p.Thr3870= | synonymous_variant | 86/105 | ||||
RYR2 | ENST00000609119.2 | c.*2714T>C | 3_prime_UTR_variant, NMD_transcript_variant | 85/104 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000565 AC: 1AN: 176854Hom.: 0 AF XY: 0.0000107 AC XY: 1AN XY: 93656
GnomAD4 exome AF: 7.20e-7 AC: 1AN: 1388570Hom.: 0 Cov.: 25 AF XY: 0.00000145 AC XY: 1AN XY: 687580
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at