10-93313049-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBS2_Supporting
The NM_013451.4(MYOF):c.5860G>A(p.Ala1954Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000632 in 1,613,080 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_013451.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYOF | NM_013451.4 | c.5860G>A | p.Ala1954Thr | missense_variant | 51/54 | ENST00000359263.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYOF | ENST00000359263.9 | c.5860G>A | p.Ala1954Thr | missense_variant | 51/54 | 1 | NM_013451.4 | P1 | |
MYOF | ENST00000358334.9 | c.5821G>A | p.Ala1941Thr | missense_variant | 50/53 | 1 | |||
MYOF | ENST00000463743.5 | c.*419G>A | 3_prime_UTR_variant, NMD_transcript_variant | 31/34 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152202Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000724 AC: 18AN: 248692Hom.: 0 AF XY: 0.0000741 AC XY: 10AN XY: 134986
GnomAD4 exome AF: 0.0000630 AC: 92AN: 1460878Hom.: 0 Cov.: 29 AF XY: 0.0000743 AC XY: 54AN XY: 726760
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152202Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 09, 2022 | The c.5860G>A (p.A1954T) alteration is located in exon 51 (coding exon 51) of the MYOF gene. This alteration results from a G to A substitution at nucleotide position 5860, causing the alanine (A) at amino acid position 1954 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at