4-145138068-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001366057.1(OTUD4):c.2707T>G(p.Cys903Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000186 in 1,614,042 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 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 -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
OTUD4 | NM_001366057.1 | c.2707T>G | p.Cys903Gly | missense_variant | 21/21 | ENST00000447906.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OTUD4 | ENST00000447906.8 | c.2707T>G | p.Cys903Gly | missense_variant | 21/21 | 5 | NM_001366057.1 | P1 | |
OTUD4 | ENST00000454497.6 | c.2512T>G | p.Cys838Gly | missense_variant | 21/21 | 2 | |||
OTUD4 | ENST00000455611.6 | n.2028+1883T>G | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152220Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251212Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135800
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461822Hom.: 1 Cov.: 33 AF XY: 0.0000206 AC XY: 15AN XY: 727222
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152220Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 23, 2023 | The c.2512T>G (p.C838G) alteration is located in exon 21 (coding exon 20) of the OTUD4 gene. This alteration results from a T to G substitution at nucleotide position 2512, causing the cysteine (C) at amino acid position 838 to be replaced by a glycine (G). 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