chr11-17635638-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_ModerateBP6_Very_StrongBP7
The NM_001292063.2(OTOG):c.7722C>T(p.Pro2574=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000148 in 1,550,410 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. P2574P) has been classified as Likely benign.
Frequency
Consequence
NM_001292063.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OTOG | NM_001292063.2 | c.7722C>T | p.Pro2574= | synonymous_variant | 47/56 | ENST00000399397.6 | |
OTOG | NM_001277269.2 | c.7758C>T | p.Pro2586= | synonymous_variant | 46/55 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OTOG | ENST00000399397.6 | c.7722C>T | p.Pro2574= | synonymous_variant | 47/56 | 5 | NM_001292063.2 | P2 | |
OTOG | ENST00000399391.7 | c.7758C>T | p.Pro2586= | synonymous_variant | 46/55 | 5 | A2 | ||
OTOG | ENST00000342528.2 | n.4634C>T | non_coding_transcript_exon_variant | 20/22 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152192Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000134 AC: 2AN: 148890Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 80214
GnomAD4 exome AF: 0.0000136 AC: 19AN: 1398218Hom.: 0 Cov.: 31 AF XY: 0.00000870 AC XY: 6AN XY: 689646
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152192Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74354
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 22, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 07, 2021 | See Variant Classification Assertion Criteria. - |
Autosomal recessive nonsyndromic hearing loss 18B Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | WangQJ Lab, Chinese People's Liberation Army General Hospital | Jul 01, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at