16-21678571-A-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6BP7
The NM_144672.4(OTOA):c.57A>T(p.Gly19=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000434 in 1,613,674 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 Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. G19G) has been classified as Likely benign.
Frequency
Consequence
NM_144672.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OTOA | NM_144672.4 | c.57A>T | p.Gly19= | synonymous_variant | 2/29 | ENST00000646100.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OTOA | ENST00000646100.2 | c.57A>T | p.Gly19= | synonymous_variant | 2/29 | NM_144672.4 | P2 | ||
OTOA | ENST00000388958.8 | c.57A>T | p.Gly19= | synonymous_variant | 1/28 | 1 | P2 | ||
OTOA | ENST00000286149.8 | c.57A>T | p.Gly19= | synonymous_variant | 1/28 | 5 | A2 | ||
OTOA | ENST00000647277.1 | c.57A>T | p.Gly19= | synonymous_variant, NMD_transcript_variant | 2/29 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151864Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251468Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135912
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461810Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3AN XY: 727216
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151864Hom.: 0 Cov.: 32 AF XY: 0.0000270 AC XY: 2AN XY: 74146
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 18, 2023 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jan 18, 2021 | Has not been previously published as pathogenic or benign to our knowledge; In silico analysis, which includes splice predictors and evolutionary conservation, suggests this variant may impact gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at