chr4-681930-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.458C>T(p.Ala153Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000179 in 1,325,934 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict 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. A153P) has been classified 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.458C>T | p.Ala153Val | missense_variant | 9/9 | ENST00000400159.7 | |
SLC49A3 | NM_032219.4 | c.*28G>A | 3_prime_UTR_variant | 10/10 | ENST00000322224.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYL5 | ENST00000400159.7 | c.458C>T | p.Ala153Val | missense_variant | 9/9 | 1 | NM_002477.2 | P1 | |
SLC49A3 | ENST00000322224.9 | c.*28G>A | 3_prime_UTR_variant | 10/10 | 1 | NM_032219.4 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000856 AC: 13AN: 151948Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000150 AC: 17AN: 113312Hom.: 0 AF XY: 0.000179 AC XY: 11AN XY: 61288
GnomAD4 exome AF: 0.000191 AC: 224AN: 1173876Hom.: 0 Cov.: 31 AF XY: 0.000223 AC XY: 126AN XY: 565028
GnomAD4 genome ? AF: 0.0000855 AC: 13AN: 152058Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 07, 2024 | The c.458C>T (p.A153V) alteration is located in exon 7 (coding exon 7) of the MYL5 gene. This alteration results from a C to T substitution at nucleotide position 458, causing the alanine (A) at amino acid position 153 to be replaced by a valine (V). 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