chr4-145137776-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001366057.1(OTUD4):c.2999C>T(p.Thr1000Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,854 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T1000N) has been classified 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.2999C>T | p.Thr1000Ile | missense_variant | 21/21 | ENST00000447906.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
OTUD4 | ENST00000447906.8 | c.2999C>T | p.Thr1000Ile | missense_variant | 21/21 | 5 | NM_001366057.1 | P1 | |
OTUD4 | ENST00000454497.6 | c.2804C>T | p.Thr935Ile | missense_variant | 21/21 | 2 | |||
OTUD4 | ENST00000455611.6 | n.2028+2175C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461854Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 727226
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 04, 2022 | The c.2804C>T (p.T935I) alteration is located in exon 21 (coding exon 20) of the OTUD4 gene. This alteration results from a C to T substitution at nucleotide position 2804, causing the threonine (T) at amino acid position 935 to be replaced by an isoleucine (I). 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
Publications
No publications associated with this variant yet.