10-93310574-G-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6BP7BS2
The NM_013451.4(MYOF):c.5959C>A(p.Arg1987Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000317 in 1,613,726 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 (no stars).
Frequency
Consequence
NM_013451.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MYOF | ENST00000359263.9 | c.5959C>A | p.Arg1987Arg | synonymous_variant | Exon 52 of 54 | 1 | NM_013451.4 | ENSP00000352208.4 | ||
MYOF | ENST00000358334.9 | c.5920C>A | p.Arg1974Arg | synonymous_variant | Exon 51 of 53 | 1 | ENSP00000351094.5 | |||
MYOF | ENST00000463743.5 | n.*518C>A | non_coding_transcript_exon_variant | Exon 32 of 34 | 5 | ENSP00000432708.1 | ||||
MYOF | ENST00000463743.5 | n.*518C>A | 3_prime_UTR_variant | Exon 32 of 34 | 5 | ENSP00000432708.1 |
Frequencies
GnomAD3 genomes AF: 0.000197 AC: 30AN: 152148Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000172 AC: 43AN: 249462Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 135346
GnomAD4 exome AF: 0.000329 AC: 481AN: 1461460Hom.: 0 Cov.: 31 AF XY: 0.000300 AC XY: 218AN XY: 727006
GnomAD4 genome AF: 0.000197 AC: 30AN: 152266Hom.: 0 Cov.: 32 AF XY: 0.000201 AC XY: 15AN XY: 74464
ClinVar
Submissions by phenotype
MYOF-related disorder Benign:1
This variant is classified as likely 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