4-52628039-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PM2PP2PP3BP4
The NM_022832.4(USP46):c.242C>T(p.Ala81Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000806 in 1,613,860 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_022832.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USP46 | NM_022832.4 | c.242C>T | p.Ala81Val | missense_variant | 3/9 | ENST00000441222.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USP46 | ENST00000441222.8 | c.242C>T | p.Ala81Val | missense_variant | 3/9 | 1 | NM_022832.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000289 AC: 44AN: 152180Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000117 AC: 29AN: 248840Hom.: 0 AF XY: 0.0000519 AC XY: 7AN XY: 135004
GnomAD4 exome AF: 0.0000582 AC: 85AN: 1461562Hom.: 0 Cov.: 30 AF XY: 0.0000509 AC XY: 37AN XY: 727074
GnomAD4 genome ? AF: 0.000295 AC: 45AN: 152298Hom.: 0 Cov.: 33 AF XY: 0.000269 AC XY: 20AN XY: 74464
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 12, 2021 | The c.242C>T (p.A81V) alteration is located in exon 3 (coding exon 3) of the USP46 gene. This alteration results from a C to T substitution at nucleotide position 242, causing the alanine (A) at amino acid position 81 to be replaced by a valine (V). 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