rs2272069
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_ModerateBP6_Very_StrongBP7
The NM_194248.3(OTOF):c.2580C>T(p.Val860=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000435 in 1,610,928 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. V860V) has been classified as Benign.
Frequency
Consequence
NM_194248.3 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OTOF | NM_194248.3 | c.2580C>T | p.Val860= | synonymous_variant | 22/47 | ENST00000272371.7 | NP_919224.1 | |
OTOF | NM_194323.3 | c.339C>T | p.Val113= | synonymous_variant | 5/29 | ENST00000339598.8 | NP_919304.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
OTOF | ENST00000272371.7 | c.2580C>T | p.Val860= | synonymous_variant | 22/47 | 1 | NM_194248.3 | ENSP00000272371 | A1 | |
OTOF | ENST00000339598.8 | c.339C>T | p.Val113= | synonymous_variant | 5/29 | 1 | NM_194323.3 | ENSP00000344521 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151594Hom.: 0 Cov.: 29
GnomAD3 exomes AF: 0.00000807 AC: 2AN: 247854Hom.: 0 AF XY: 0.00000743 AC XY: 1AN XY: 134624
GnomAD4 exome AF: 0.00000343 AC: 5AN: 1459334Hom.: 0 Cov.: 36 AF XY: 0.00000275 AC XY: 2AN XY: 725956
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151594Hom.: 0 Cov.: 29 AF XY: 0.0000135 AC XY: 1AN XY: 74054
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Sep 21, 2023 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 19, 2018 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at