rs568549806
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong
The NM_001292063.2(OTOG):c.6907C>T(p.Arg2303Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0011 in 1,550,218 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R2303H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001292063.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OTOG | NM_001292063.2 | c.6907C>T | p.Arg2303Cys | missense_variant | 41/56 | ENST00000399397.6 | |
OTOG | NM_001277269.2 | c.6943C>T | p.Arg2315Cys | missense_variant | 40/55 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OTOG | ENST00000399397.6 | c.6907C>T | p.Arg2303Cys | missense_variant | 41/56 | 5 | NM_001292063.2 | P2 | |
OTOG | ENST00000399391.7 | c.6943C>T | p.Arg2315Cys | missense_variant | 40/55 | 5 | A2 | ||
OTOG | ENST00000342528.2 | n.4245C>T | non_coding_transcript_exon_variant | 17/22 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00106 AC: 162AN: 152224Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00115 AC: 171AN: 148548Hom.: 1 AF XY: 0.00115 AC XY: 92AN XY: 80002
GnomAD4 exome AF: 0.00110 AC: 1543AN: 1397876Hom.: 2 Cov.: 32 AF XY: 0.00111 AC XY: 766AN XY: 689468
GnomAD4 genome ? AF: 0.00106 AC: 162AN: 152342Hom.: 0 Cov.: 32 AF XY: 0.00114 AC XY: 85AN XY: 74494
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 27, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 08, 2021 | See Variant Classification Assertion Criteria. - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 12, 2018 | p.Arg2315Cys in exon 40 of OTOG: This variant is classified as likely benign bec ause it has been identified in 0.3% (59/19838) of European Finnish chromosomes b y the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs568549806). ACMG criteria applied: PP3; BS1 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at