chr13-108665916-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001198950.3(MYO16):c.59C>A(p.Ser20Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.000000684 in 1,461,576 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. S20S) has been classified as Likely benign.
Frequency
Consequence
NM_001198950.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MYO16 | NM_001198950.3 | c.59C>A | p.Ser20Tyr | missense_variant | 2/35 | ENST00000457511.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MYO16 | ENST00000457511.7 | c.59C>A | p.Ser20Tyr | missense_variant | 2/35 | 1 | NM_001198950.3 | A2 | |
MYO16 | ENST00000356711.7 | c.-8C>A | 5_prime_UTR_variant | 2/35 | 1 | P2 | |||
MYO16 | ENST00000251041.10 | c.-8C>A | 5_prime_UTR_variant | 2/25 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250908Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135612
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461576Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727098
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 09, 2024 | The c.59C>A (p.S20Y) alteration is located in exon 2 (coding exon 2) of the MYO16 gene. This alteration results from a C to A substitution at nucleotide position 59, causing the serine (S) at amino acid position 20 to be replaced by a tyrosine (Y). 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