2-26484494-G-T
Variant summary
Our verdict is Benign. Variant got -17 ACMG points: 0P and 17B. BP4_StrongBP6_Very_StrongBP7BS2
The NM_194248.3(OTOF):c.1185C>A(p.Thr395=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000179 in 1,614,028 control chromosomes in the GnomAD database, including 3 homozygotes. 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. T395T) has been classified as Likely benign.
Frequency
Consequence
NM_194248.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OTOF | NM_194248.3 | c.1185C>A | p.Thr395= | synonymous_variant | 12/47 | ENST00000272371.7 | |
OTOF | NM_001287489.2 | c.1185C>A | p.Thr395= | synonymous_variant | 12/46 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OTOF | ENST00000272371.7 | c.1185C>A | p.Thr395= | synonymous_variant | 12/47 | 1 | NM_194248.3 | A1 | |
OTOF | ENST00000403946.7 | c.1185C>A | p.Thr395= | synonymous_variant | 12/46 | 5 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152182Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000343 AC: 86AN: 250480Hom.: 2 AF XY: 0.000413 AC XY: 56AN XY: 135730
GnomAD4 exome AF: 0.000192 AC: 280AN: 1461728Hom.: 3 Cov.: 32 AF XY: 0.000279 AC XY: 203AN XY: 727148
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152300Hom.: 0 Cov.: 33 AF XY: 0.0000806 AC XY: 6AN XY: 74462
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 12, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 27, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at