19-38455575-G-C
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_000540.3(RYR1):c.1672+29G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.654 in 1,611,946 control chromosomes in the GnomAD database, including 347,871 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_000540.3 intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
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RYR1 | ENST00000359596.8 | c.1672+29G>C | intron_variant | Intron 15 of 105 | 5 | NM_000540.3 | ENSP00000352608.2 | |||
RYR1 | ENST00000355481.8 | c.1672+29G>C | intron_variant | Intron 15 of 104 | 1 | ENSP00000347667.3 | ||||
RYR1 | ENST00000599547.6 | n.1672+29G>C | intron_variant | Intron 15 of 79 | 2 | ENSP00000471601.2 |
Frequencies
GnomAD3 genomes AF: 0.638 AC: 96909AN: 151846Hom.: 31441 Cov.: 31
GnomAD3 exomes AF: 0.642 AC: 161425AN: 251250Hom.: 52754 AF XY: 0.637 AC XY: 86438AN XY: 135788
GnomAD4 exome AF: 0.655 AC: 956796AN: 1459982Hom.: 316420 Cov.: 37 AF XY: 0.650 AC XY: 472408AN XY: 726440
GnomAD4 genome AF: 0.638 AC: 96962AN: 151964Hom.: 31451 Cov.: 31 AF XY: 0.635 AC XY: 47171AN XY: 74254
ClinVar
Submissions by phenotype
not provided Benign:2Other:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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not specified Benign:1
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Congenital multicore myopathy with external ophthalmoplegia Benign:1
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King Denborough syndrome Benign:1
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Central core myopathy Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at