rs147901051
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_144672.4(OTOA):c.2019C>T(p.Asp673=) variant causes a splice region, synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000477 in 1,614,134 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_144672.4 splice_region, 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OTOA | NM_144672.4 | c.2019C>T | p.Asp673= | splice_region_variant, synonymous_variant | 20/29 | ENST00000646100.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OTOA | ENST00000646100.2 | c.2019C>T | p.Asp673= | splice_region_variant, synonymous_variant | 20/29 | NM_144672.4 | P2 |
Frequencies
GnomAD3 genomes AF: 0.000197 AC: 30AN: 152150Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.0000796 AC: 20AN: 251284Hom.: 0 AF XY: 0.0000810 AC XY: 11AN XY: 135800
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1461866Hom.: 0 Cov.: 31 AF XY: 0.0000289 AC XY: 21AN XY: 727236
GnomAD4 genome AF: 0.000197 AC: 30AN: 152268Hom.: 1 Cov.: 32 AF XY: 0.000215 AC XY: 16AN XY: 74456
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Apr 30, 2012 | Asp673Asp in Exon 19 of OTOA: This variant is not expected to have clinical sign ificance because it does not alter an amino acid residue, is not located within the splice consensus sequence, and has been identified in 1/3738 African America n chromosomes from a broad population by the NHLBI Exome Sequencing Project (htt p://evs.gs.washington.edu/EVS; dbSNP rs147901051). - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 17, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at