12-80341966-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001378609.3(OTOGL):c.5069C>T(p.Pro1690Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000357 in 1,604,484 control chromosomes in the GnomAD database, including 4 homozygotes. 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. P1690P) has been classified as Likely benign.
Frequency
Consequence
NM_001378609.3 missense
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.5069C>T | p.Pro1690Leu | missense_variant | 44/59 | ENST00000547103.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OTOGL | ENST00000547103.7 | c.5069C>T | p.Pro1690Leu | missense_variant | 44/59 | 5 | NM_001378609.3 | P1 | |
OTOGL | ENST00000646859.1 | c.4934C>T | p.Pro1645Leu | missense_variant | 48/63 | ||||
OTOGL | ENST00000298820.7 | c.371C>T | p.Pro124Leu | missense_variant | 5/18 | 5 |
Frequencies
GnomAD3 genomes AF: 0.000323 AC: 49AN: 151920Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000567 AC: 134AN: 236456Hom.: 2 AF XY: 0.000563 AC XY: 72AN XY: 127906
GnomAD4 exome AF: 0.000361 AC: 524AN: 1452446Hom.: 4 Cov.: 29 AF XY: 0.000366 AC XY: 264AN XY: 721892
GnomAD4 genome AF: 0.000316 AC: 48AN: 152038Hom.: 0 Cov.: 32 AF XY: 0.000323 AC XY: 24AN XY: 74300
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 12, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 24, 2021 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | May 07, 2015 | p.Pro1681Leu in exon 43 of OTOGL: This variant is not expected to have clinical significance because it has been identified in 1.2% (65/5238) of East Asian chro mosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.or g; dbSNP rs185895624). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at