1-77714740-T-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_201624.3(USP33):āc.2089A>Cā(p.Asn697His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000057 in 1,612,626 control chromosomes in the GnomAD database, including 3 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 (ā ).
Frequency
Consequence
NM_201624.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USP33 | NM_201624.3 | c.2089A>C | p.Asn697His | missense_variant | 19/24 | ENST00000370794.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USP33 | ENST00000370794.7 | c.2089A>C | p.Asn697His | missense_variant | 19/24 | 1 | NM_201624.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152230Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000916 AC: 23AN: 251072Hom.: 0 AF XY: 0.000133 AC XY: 18AN XY: 135698
GnomAD4 exome AF: 0.0000609 AC: 89AN: 1460278Hom.: 3 Cov.: 30 AF XY: 0.0000950 AC XY: 69AN XY: 726452
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152348Hom.: 0 Cov.: 32 AF XY: 0.0000268 AC XY: 2AN XY: 74502
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 30, 2023 | The c.2182A>C (p.N728H) alteration is located in exon 20 (coding exon 19) of the USP33 gene. This alteration results from a A to C substitution at nucleotide position 2182, causing the asparagine (N) at amino acid position 728 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