chr10-93313135-G-A
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_013451.4(MYOF):c.5774C>T(p.Pro1925Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000232 in 1,614,080 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 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 Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYOF | NM_013451.4 | c.5774C>T | p.Pro1925Leu | missense_variant | 51/54 | ENST00000359263.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYOF | ENST00000359263.9 | c.5774C>T | p.Pro1925Leu | missense_variant | 51/54 | 1 | NM_013451.4 | P1 | |
MYOF | ENST00000358334.9 | c.5735C>T | p.Pro1912Leu | missense_variant | 50/53 | 1 | |||
MYOF | ENST00000463743.5 | c.*333C>T | 3_prime_UTR_variant, NMD_transcript_variant | 31/34 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000230 AC: 35AN: 152178Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000325 AC: 81AN: 249440Hom.: 0 AF XY: 0.000325 AC XY: 44AN XY: 135334
GnomAD4 exome AF: 0.000232 AC: 339AN: 1461784Hom.: 0 Cov.: 29 AF XY: 0.000232 AC XY: 169AN XY: 727194
GnomAD4 genome ? AF: 0.000230 AC: 35AN: 152296Hom.: 0 Cov.: 33 AF XY: 0.000228 AC XY: 17AN XY: 74480
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 04, 2022 | The c.5774C>T (p.P1925L) alteration is located in exon 51 (coding exon 51) of the MYOF gene. This alteration results from a C to T substitution at nucleotide position 5774, causing the proline (P) at amino acid position 1925 to be replaced by a leucine (L). 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