rs727503313
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_016239.4(MYO15A):c.6864G>A(p.Ser2288Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000579 in 1,607,342 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 Likely benign (★★).
Frequency
Consequence
NM_016239.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MYO15A | NM_016239.4 | c.6864G>A | p.Ser2288Ser | synonymous_variant | Exon 33 of 66 | ENST00000647165.2 | NP_057323.3 | |
MYO15A | XM_017024715.3 | c.6867G>A | p.Ser2289Ser | synonymous_variant | Exon 31 of 64 | XP_016880204.1 | ||
MYO15A | XM_017024714.3 | c.6804G>A | p.Ser2268Ser | synonymous_variant | Exon 30 of 63 | XP_016880203.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152178Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000554 AC: 13AN: 234754Hom.: 0 AF XY: 0.0000548 AC XY: 7AN XY: 127688
GnomAD4 exome AF: 0.0000591 AC: 86AN: 1455164Hom.: 0 Cov.: 34 AF XY: 0.0000636 AC XY: 46AN XY: 723222
GnomAD4 genome AF: 0.0000460 AC: 7AN: 152178Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74346
ClinVar
Submissions by phenotype
not specified Benign:1
Ser2288Ser in exon 33 of MYO15A: This variant is not expected to have clinical s ignificance because it does not alter an amino acid residue and is not located w ithin the splice consensus sequence. -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at