chr11-17634154-A-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The NM_001292063.2(OTOG):āc.7353A>Cā(p.Gln2451His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000208 in 1,549,856 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ā ).
Frequency
Consequence
NM_001292063.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OTOG | NM_001292063.2 | c.7353A>C | p.Gln2451His | missense_variant | 44/56 | ENST00000399397.6 | |
OTOG | NM_001277269.2 | c.7389A>C | p.Gln2463His | missense_variant | 43/55 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OTOG | ENST00000399397.6 | c.7353A>C | p.Gln2451His | missense_variant | 44/56 | 5 | NM_001292063.2 | P2 | |
OTOG | ENST00000399391.7 | c.7389A>C | p.Gln2463His | missense_variant | 43/55 | 5 | A2 | ||
OTOG | ENST00000342528.2 | n.4605+280A>C | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00127 AC: 193AN: 152020Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000177 AC: 26AN: 146710Hom.: 0 AF XY: 0.000114 AC XY: 9AN XY: 79158
GnomAD4 exome AF: 0.0000923 AC: 129AN: 1397718Hom.: 0 Cov.: 32 AF XY: 0.0000740 AC XY: 51AN XY: 689408
GnomAD4 genome ? AF: 0.00127 AC: 193AN: 152138Hom.: 0 Cov.: 32 AF XY: 0.00114 AC XY: 85AN XY: 74384
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 | Nov 15, 2017 | p.Gln2463His in exon 43 of OTOG: This variant is not expected to have clinical s ignificance because it has been identified in 0.4% (62/15180) of African chromos omeschromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadi nstitute.org; dbSNP rs145833172). - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 25, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at