rs777658929
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_194248.3(OTOF):āc.3870T>Cā(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 (ā ). 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