chr9-129868177-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001110303.4(USP20):c.863C>T(p.Ser288Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000682 in 1,613,916 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. S288S) has been classified as Benign.
Frequency
Consequence
NM_001110303.4 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 |
---|---|---|---|---|---|---|---|
USP20 | NM_001110303.4 | c.863C>T | p.Ser288Leu | missense_variant | 11/26 | ENST00000372429.8 | |
USP20 | NM_001008563.5 | c.863C>T | p.Ser288Leu | missense_variant | 11/26 | ||
USP20 | NM_006676.8 | c.863C>T | p.Ser288Leu | missense_variant | 11/25 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USP20 | ENST00000372429.8 | c.863C>T | p.Ser288Leu | missense_variant | 11/26 | 1 | NM_001110303.4 | P1 | |
USP20 | ENST00000315480.9 | c.863C>T | p.Ser288Leu | missense_variant | 11/25 | 1 | P1 | ||
USP20 | ENST00000358355.5 | c.863C>T | p.Ser288Leu | missense_variant | 11/26 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152138Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 249346Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135290
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461778Hom.: 0 Cov.: 90 AF XY: 0.00000550 AC XY: 4AN XY: 727192
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152138Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74318
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 13, 2021 | The c.863C>T (p.S288L) alteration is located in exon 11 (coding exon 9) of the USP20 gene. This alteration results from a C to T substitution at nucleotide position 863, causing the serine (S) at amino acid position 288 to be replaced by a leucine (L). 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