rs367996419
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM2BP4_StrongBP6_Very_StrongBS1
The NM_001378609.3(OTOGL):c.1441+10T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000849 in 1,599,000 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.00062 ( 0 hom., cov: 32)
Exomes 𝑓: 0.00087 ( 0 hom. )
Consequence
OTOGL
NM_001378609.3 intron
NM_001378609.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.154
Genes affected
OTOGL (HGNC:26901): (otogelin like) The protein encoded by this gene belongs to the otogelin family. This gene is expressed in the inner ear of vertebrates with the highest level of expression seen at the embryonic stage and lowest in adult. Knockdown studies in zebrafish suggest that this gene is essential for normal inner ear function. Mutations in this gene are associated with autosomal recessive deafness. [provided by RefSeq, Dec 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BP6
Variant 12-80254580-T-A is Benign according to our data. Variant chr12-80254580-T-A is described in ClinVar as [Benign]. Clinvar id is 227811.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-80254580-T-A is described in Lovd as [Likely_benign].
BS1
Variant frequency is greater than expected in population amr. gnomad4_exome allele frequency = 0.000874 (1264/1446948) while in subpopulation AMR AF= 0.0038 (169/44474). AF 95% confidence interval is 0.00333. There are 0 homozygotes in gnomad4_exome. There are 613 alleles in male gnomad4_exome subpopulation. Median coverage is 29. This position pass quality control queck.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OTOGL | NM_001378609.3 | c.1441+10T>A | intron_variant | ENST00000547103.7 | NP_001365538.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OTOGL | ENST00000547103.7 | c.1441+10T>A | intron_variant | 5 | NM_001378609.3 | ENSP00000447211 | P1 | |||
OTOGL | ENST00000646859.1 | c.1441+10T>A | intron_variant | ENSP00000496036 | ||||||
OTOGL | ENST00000643417.1 | n.2101+10T>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.000619 AC: 94AN: 151934Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000981 AC: 240AN: 244652Hom.: 0 AF XY: 0.000917 AC XY: 122AN XY: 132980
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GnomAD4 exome AF: 0.000874 AC: 1264AN: 1446948Hom.: 0 Cov.: 29 AF XY: 0.000851 AC XY: 613AN XY: 720140
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GnomAD4 genome AF: 0.000618 AC: 94AN: 152052Hom.: 0 Cov.: 32 AF XY: 0.000673 AC XY: 50AN XY: 74338
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jun 13, 2017 | c.1414+10T>A in intron 14 of OTOGL: This variant is not expected to have clinica l significance because it is not located within the splice consensus sequence. I t has been identified in 0.4% (131/34138) of Latino chromosomes by the Genome Ag gregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs367996419) . - |
OTOGL-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 31, 2019 | This variant is classified as likely 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 | Labcorp Genetics (formerly Invitae), Labcorp | Jan 11, 2024 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at