rs777658929
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_194248.3(OTOF):c.3870T>C(p.Ser1290=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000616 in 1,461,794 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. S1290S) has been classified as Likely benign.
Frequency
Consequence
NM_194248.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OTOF | NM_194248.3 | c.3870T>C | p.Ser1290= | synonymous_variant | 31/47 | ENST00000272371.7 | |
OTOF | NM_194323.3 | c.1569T>C | p.Ser523= | synonymous_variant | 14/29 | ENST00000339598.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OTOF | ENST00000272371.7 | c.3870T>C | p.Ser1290= | synonymous_variant | 31/47 | 1 | NM_194248.3 | A1 | |
OTOF | ENST00000339598.8 | c.1569T>C | p.Ser523= | synonymous_variant | 14/29 | 1 | NM_194323.3 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.0000278 AC: 7AN: 251368Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135850
GnomAD4 exome AF: 0.00000616 AC: 9AN: 1461794Hom.: 0 Cov.: 32 AF XY: 0.00000550 AC XY: 4AN XY: 727182
GnomAD4 genome ? Cov.: 33
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 | Nov 01, 2016 | p.Ser1290Ser in exon 31 of OTOF: This variant is not expected to have clinical s ignificance because it does not alter an amino acid residue and is not located w ithin the splice consensus sequence. It has been identified in 3/11574 Latino ch romosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute. org; dbSNP rs777658929). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at