rs113745835
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001292063.2(OTOG):c.2098G>A(p.Ala700Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000867 in 1,548,268 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001292063.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OTOG | NM_001292063.2 | c.2098G>A | p.Ala700Thr | missense_variant | 19/56 | ENST00000399397.6 | |
OTOG | NM_001277269.2 | c.2134G>A | p.Ala712Thr | missense_variant | 18/55 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OTOG | ENST00000399397.6 | c.2098G>A | p.Ala700Thr | missense_variant | 19/56 | 5 | NM_001292063.2 | P2 | |
OTOG | ENST00000399391.7 | c.2134G>A | p.Ala712Thr | missense_variant | 18/55 | 5 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00429 AC: 653AN: 152136Hom.: 4 Cov.: 33
GnomAD3 exomes AF: 0.00113 AC: 164AN: 145464Hom.: 2 AF XY: 0.000803 AC XY: 63AN XY: 78502
GnomAD4 exome AF: 0.000489 AC: 683AN: 1396014Hom.: 8 Cov.: 32 AF XY: 0.000407 AC XY: 280AN XY: 688660
GnomAD4 genome ? AF: 0.00433 AC: 659AN: 152254Hom.: 5 Cov.: 33 AF XY: 0.00422 AC XY: 314AN XY: 74444
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | GeneDx | Feb 05, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 02, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | Athena Diagnostics | Nov 12, 2018 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jul 21, 2015 | p.Ala712Thr in exon 18 of OTOG: This variant is not expected to have clinical si gnificance because it has been identified in 1.6% (15/918) of African chromosome s by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbS NP rs113745835). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at