12-80336990-C-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2BP4BP6_Moderate
The NM_001378609.3(OTOGL):c.4846C>A(p.Arg1616=) variant causes a synonymous change. The variant allele was found at a frequency of 0.0000042 in 1,428,240 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 Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. R1616R) has been classified as Likely benign.
Frequency
Consequence
NM_001378609.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OTOGL | NM_001378609.3 | c.4846C>A | p.Arg1616= | synonymous_variant | 42/59 | ENST00000547103.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OTOGL | ENST00000547103.7 | c.4846C>A | p.Arg1616= | synonymous_variant | 42/59 | 5 | NM_001378609.3 | P1 | |
OTOGL | ENST00000646859.1 | c.4711C>A | p.Arg1571= | synonymous_variant | 46/63 | ||||
OTOGL | ENST00000298820.7 | c.148C>A | p.Arg50= | synonymous_variant | 3/18 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000101 AC: 2AN: 198178Hom.: 0 AF XY: 0.00000944 AC XY: 1AN XY: 105916
GnomAD4 exome AF: 0.00000420 AC: 6AN: 1428240Hom.: 0 Cov.: 32 AF XY: 0.00000848 AC XY: 6AN XY: 707470
GnomAD4 genome Cov.: 32
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 | Mar 20, 2016 | p.Arg1607Arg in exon 41 of OTOGL: This variant is not expected to have clinical significance because it does not alter an amino acid residue and is not located within the splice consensus sequence. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at