8-91071227-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_016023.5(OTUD6B):c.172G>A(p.Glu58Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000223 in 1,613,884 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016023.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OTUD6B | NM_016023.5 | c.172G>A | p.Glu58Lys | missense_variant | Exon 2 of 7 | ENST00000404789.8 | NP_057107.4 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152196Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 251104Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135718
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461570Hom.: 1 Cov.: 32 AF XY: 0.00000963 AC XY: 7AN XY: 727076
GnomAD4 genome AF: 0.000105 AC: 16AN: 152314Hom.: 0 Cov.: 33 AF XY: 0.0000671 AC XY: 5AN XY: 74480
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.262G>A (p.E88K) alteration is located in exon 2 (coding exon 2) of the OTUD6B gene. This alteration results from a G to A substitution at nucleotide position 262, causing the glutamic acid (E) at amino acid position 88 to be replaced by a lysine (K). Based on data from the Genome Aggregation Database (gnomAD) database, the OTUD6B c.262G>A alteration was observed in 0.004% (11/282486) of total alleles studied, with a frequency of 0.04% (10/24966) in the African subpopulation. This amino acid position is not well conserved in available vertebrate species. The in silico prediction for the p.E88K alteration is inconclusive. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at