8-91070370-G-A
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The ENST00000285420.8(OTUD6B):c.76G>A(p.Gly26Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00233 in 1,612,012 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
ENST00000285420.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
OTUD6B | NM_016023.5 | c.-15G>A | 5_prime_UTR_variant | Exon 1 of 7 | ENST00000404789.8 | NP_057107.4 | ||
OTUD6B | NM_001416022.1 | c.-15G>A | 5_prime_UTR_variant | Exon 1 of 6 | NP_001402951.1 | |||
OTUD6B | NM_001286745.3 | c.-458G>A | 5_prime_UTR_variant | Exon 1 of 8 | NP_001273674.1 | |||
OTUD6B | XM_047421864.1 | c.-15G>A | 5_prime_UTR_variant | Exon 1 of 4 | XP_047277820.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00130 AC: 198AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00133 AC: 328AN: 245972Hom.: 0 AF XY: 0.00150 AC XY: 199AN XY: 132998
GnomAD4 exome AF: 0.00243 AC: 3550AN: 1459726Hom.: 11 Cov.: 31 AF XY: 0.00238 AC XY: 1731AN XY: 725892
GnomAD4 genome AF: 0.00130 AC: 198AN: 152286Hom.: 0 Cov.: 32 AF XY: 0.00121 AC XY: 90AN XY: 74450
ClinVar
Submissions by phenotype
Intellectual developmental disorder with dysmorphic facies, seizures, and distal limb anomalies Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | Mar 03, 2018 | This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 21, 2024 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at