rs1551122
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001378609.3(OTOGL):āc.6737A>Gā(p.Asn2246Ser) variant causes a missense, splice region change. The variant allele was found at a frequency of 0.608 in 1,538,726 control chromosomes in the GnomAD database, including 294,099 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 (ā ā ). Synonymous variant affecting the same amino acid position (i.e. N2246N) has been classified as Likely benign.
Frequency
Consequence
NM_001378609.3 missense, splice_region
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 |
---|---|---|---|---|---|---|---|
OTOGL | NM_001378609.3 | c.6737A>G | p.Asn2246Ser | missense_variant, splice_region_variant | 57/59 | ENST00000547103.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OTOGL | ENST00000547103.7 | c.6737A>G | p.Asn2246Ser | missense_variant, splice_region_variant | 57/59 | 5 | NM_001378609.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.503 AC: 76353AN: 151816Hom.: 22245 Cov.: 32
GnomAD3 exomes AF: 0.581 AC: 122147AN: 210322Hom.: 37632 AF XY: 0.597 AC XY: 68609AN XY: 114888
GnomAD4 exome AF: 0.619 AC: 859074AN: 1386792Hom.: 271855 Cov.: 28 AF XY: 0.622 AC XY: 429197AN XY: 690076
GnomAD4 genome ? AF: 0.503 AC: 76365AN: 151934Hom.: 22244 Cov.: 32 AF XY: 0.508 AC XY: 37717AN XY: 74270
ClinVar
Submissions by phenotype
not specified Benign:4
Benign, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
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. - |
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Nov 24, 2014 | Asn2237Ser in exon 56 of OTOGL: This variant is not expected to have clinical si gnificance because it has been identified in 35.9% (3089/8598) of European Ameri can chromosomes from a broad population by the NHLBI Exome Sequencing Project (h ttp://evs.gs.washington.edu/EVS; dbSNP rs1551122). - |
Benign, no assertion criteria provided | clinical testing | Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen | - | - - |
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