rs11024353
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001292063.2(OTOG):c.7894+8C>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0401 in 1,549,324 control chromosomes in the GnomAD database, including 1,437 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001292063.2 splice_region, intron
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.7894+8C>T | splice_region_variant, intron_variant | ENST00000399397.6 | |||
OTOG | NM_001277269.2 | c.7930+8C>T | splice_region_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OTOG | ENST00000399397.6 | c.7894+8C>T | splice_region_variant, intron_variant | 5 | NM_001292063.2 | P2 | |||
OTOG | ENST00000399391.7 | c.7930+8C>T | splice_region_variant, intron_variant | 5 | A2 | ||||
OTOG | ENST00000342528.2 | n.4806+8C>T | splice_region_variant, intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0397 AC: 6041AN: 152078Hom.: 138 Cov.: 32
GnomAD3 exomes AF: 0.0442 AC: 6542AN: 147882Hom.: 215 AF XY: 0.0462 AC XY: 3682AN XY: 79654
GnomAD4 exome AF: 0.0401 AC: 56050AN: 1397126Hom.: 1298 Cov.: 30 AF XY: 0.0413 AC XY: 28459AN XY: 689126
GnomAD4 genome ? AF: 0.0398 AC: 6051AN: 152198Hom.: 139 Cov.: 32 AF XY: 0.0418 AC XY: 3107AN XY: 74406
ClinVar
Submissions by phenotype
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Nov 24, 2014 | 7930+8C>T in intron 47 of OTOG: This variant is not expected to have clinical si gnificance because it is not located within the conserved splice consensus seque nce. It has been identified in 7.2% (14/194) of Luhya (Kenyan) chromosomes from a broad population by the 1000 Genomes Project (http://www.ncbi.nlm.nih.gov/proj ects/SNP; dbSNP rs11024353). - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 09, 2017 | 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. - |
OTOG-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Mar 29, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
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