chr2-26476977-G-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_194248.3(OTOF):c.2590C>A(p.Arg864Ser) variant causes a missense change. The variant allele was found at a frequency of 0.00000658 in 151,966 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R864C) has been classified as Likely benign.
Frequency
Consequence
NM_194248.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OTOF | NM_194248.3 | c.2590C>A | p.Arg864Ser | missense_variant | 22/47 | ENST00000272371.7 | |
OTOF | NM_194323.3 | c.349C>A | p.Arg117Ser | missense_variant | 5/29 | ENST00000339598.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OTOF | ENST00000272371.7 | c.2590C>A | p.Arg864Ser | missense_variant | 22/47 | 1 | NM_194248.3 | A1 | |
OTOF | ENST00000339598.8 | c.349C>A | p.Arg117Ser | missense_variant | 5/29 | 1 | NM_194323.3 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151966Hom.: 0 Cov.: 27
GnomAD4 exome Cov.: 31
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151966Hom.: 0 Cov.: 27 AF XY: 0.0000135 AC XY: 1AN XY: 74226
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at