4-679965-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002477.2(MYL5):c.239C>T(p.Ser80Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000106 in 1,613,528 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002477.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYL5 | NM_002477.2 | c.239C>T | p.Ser80Leu | missense_variant | 6/9 | ENST00000400159.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYL5 | ENST00000400159.7 | c.239C>T | p.Ser80Leu | missense_variant | 6/9 | 1 | NM_002477.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152184Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000600 AC: 15AN: 250074Hom.: 0 AF XY: 0.0000517 AC XY: 7AN XY: 135518
GnomAD4 exome AF: 0.000111 AC: 162AN: 1461344Hom.: 0 Cov.: 32 AF XY: 0.0000977 AC XY: 71AN XY: 727002
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152184Hom.: 0 Cov.: 33 AF XY: 0.0000673 AC XY: 5AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 17, 2021 | The c.239C>T (p.S80L) alteration is located in exon 4 (coding exon 4) of the MYL5 gene. This alteration results from a C to T substitution at nucleotide position 239, causing the serine (S) at amino acid position 80 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