chr4-145138258-C-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001366057.1(OTUD4):c.2517G>T(p.Gln839His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000719 in 1,613,828 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001366057.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OTUD4 | NM_001366057.1 | c.2517G>T | p.Gln839His | missense_variant | 21/21 | ENST00000447906.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OTUD4 | ENST00000447906.8 | c.2517G>T | p.Gln839His | missense_variant | 21/21 | 5 | NM_001366057.1 | P1 | |
OTUD4 | ENST00000454497.6 | c.2322G>T | p.Gln774His | missense_variant | 21/21 | 2 | |||
OTUD4 | ENST00000455611.6 | n.2028+1693G>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000526 AC: 8AN: 152170Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 251100Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135712
GnomAD4 exome AF: 0.0000739 AC: 108AN: 1461658Hom.: 0 Cov.: 33 AF XY: 0.0000619 AC XY: 45AN XY: 727142
GnomAD4 genome ? AF: 0.0000526 AC: 8AN: 152170Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74330
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 18, 2022 | The c.2322G>T (p.Q774H) alteration is located in exon 21 (coding exon 20) of the OTUD4 gene. This alteration results from a G to T substitution at nucleotide position 2322, causing the glutamine (Q) at amino acid position 774 to be replaced by a histidine (H). 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