rs554657199
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 2P and 13B. PM2BP4_StrongBP6_Very_StrongBP7
The NM_001292063.2(OTOG):c.6006G>A(p.Pro2002Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000497 in 1,550,518 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_001292063.2 synonymous
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OTOG | ENST00000399397.6 | c.6006G>A | p.Pro2002Pro | synonymous_variant | Exon 36 of 56 | 5 | NM_001292063.2 | ENSP00000382329.2 | ||
OTOG | ENST00000399391.7 | c.6042G>A | p.Pro2014Pro | synonymous_variant | Exon 35 of 55 | 5 | ENSP00000382323.2 | |||
OTOG | ENST00000342528.2 | n.3344G>A | non_coding_transcript_exon_variant | Exon 12 of 22 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152158Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000739 AC: 11AN: 148942Hom.: 0 AF XY: 0.0000872 AC XY: 7AN XY: 80250
GnomAD4 exome AF: 0.0000386 AC: 54AN: 1398242Hom.: 0 Cov.: 36 AF XY: 0.0000377 AC XY: 26AN XY: 689636
GnomAD4 genome AF: 0.000151 AC: 23AN: 152276Hom.: 0 Cov.: 33 AF XY: 0.000175 AC XY: 13AN XY: 74460
ClinVar
Submissions by phenotype
not specified Benign:1
p.Pro2014Pro in exon 35 of OTOG: 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. It has been identified in several populatio ns including 2/7592 South Asian chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs554657199). -
OTOG-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at