chr16-21705283-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP6_Very_StrongBS1BS2
The NM_144672.4(OTOA):c.1095C>T(p.Gly365=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00182 in 1,613,868 control chromosomes in the GnomAD database, including 53 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Synonymous variant affecting the same amino acid position (i.e. G365G) has been classified as Likely benign.
Frequency
Consequence
NM_144672.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OTOA | NM_144672.4 | c.1095C>T | p.Gly365= | synonymous_variant | 12/29 | ENST00000646100.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OTOA | ENST00000646100.2 | c.1095C>T | p.Gly365= | synonymous_variant | 12/29 | NM_144672.4 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00981 AC: 1493AN: 152126Hom.: 27 Cov.: 32
GnomAD3 exomes AF: 0.00269 AC: 676AN: 251086Hom.: 17 AF XY: 0.00196 AC XY: 266AN XY: 135690
GnomAD4 exome AF: 0.000993 AC: 1452AN: 1461624Hom.: 26 Cov.: 31 AF XY: 0.000883 AC XY: 642AN XY: 727114
GnomAD4 genome AF: 0.00979 AC: 1490AN: 152244Hom.: 27 Cov.: 32 AF XY: 0.00922 AC XY: 686AN XY: 74428
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jan 16, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | May 07, 2012 | Gly365Gly in Exon 11 of OTOA: This variant is not expected to have clinical sig nificance because it does not alter an amino acid residue, is not located within the splice consensus sequence, and has been identified in 3.5% (129/3738) of Af rican American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http://evs.gs.washington.edu/EVS; dbSNP rs115543159). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at