chr10-93313030-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_013451.4(MYOF):c.5879G>A(p.Arg1960His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000116 in 1,608,930 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1960C) has been classified 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 -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYOF | NM_013451.4 | c.5879G>A | p.Arg1960His | missense_variant | 51/54 | ENST00000359263.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYOF | ENST00000359263.9 | c.5879G>A | p.Arg1960His | missense_variant | 51/54 | 1 | NM_013451.4 | P1 | |
MYOF | ENST00000358334.9 | c.5840G>A | p.Arg1947His | missense_variant | 50/53 | 1 | |||
MYOF | ENST00000463743.5 | c.*438G>A | 3_prime_UTR_variant, NMD_transcript_variant | 31/34 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000210 AC: 32AN: 152190Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000106 AC: 26AN: 245212Hom.: 1 AF XY: 0.000105 AC XY: 14AN XY: 133022
GnomAD4 exome AF: 0.000106 AC: 154AN: 1456740Hom.: 3 Cov.: 29 AF XY: 0.0000952 AC XY: 69AN XY: 724454
GnomAD4 genome ? AF: 0.000210 AC: 32AN: 152190Hom.: 0 Cov.: 33 AF XY: 0.000229 AC XY: 17AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 26, 2022 | The c.5879G>A (p.R1960H) 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 5879, causing the arginine (R) at amino acid position 1960 to be replaced by a histidine (H). 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