9-129860944-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001110303.4(USP20):c.338C>T(p.Pro113Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000248 in 1,613,042 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001110303.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USP20 | NM_001110303.4 | c.338C>T | p.Pro113Leu | missense_variant | 7/26 | ENST00000372429.8 | |
USP20 | NM_001008563.5 | c.338C>T | p.Pro113Leu | missense_variant | 7/26 | ||
USP20 | NM_006676.8 | c.338C>T | p.Pro113Leu | missense_variant | 7/25 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USP20 | ENST00000372429.8 | c.338C>T | p.Pro113Leu | missense_variant | 7/26 | 1 | NM_001110303.4 | P1 | |
USP20 | ENST00000315480.9 | c.338C>T | p.Pro113Leu | missense_variant | 7/25 | 1 | P1 | ||
USP20 | ENST00000358355.5 | c.338C>T | p.Pro113Leu | missense_variant | 7/26 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152162Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249532Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135384
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1460880Hom.: 0 Cov.: 30 AF XY: 0.0000220 AC XY: 16AN XY: 726830
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152162Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74336
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 06, 2022 | The c.338C>T (p.P113L) alteration is located in exon 7 (coding exon 5) of the USP20 gene. This alteration results from a C to T substitution at nucleotide position 338, causing the proline (P) at amino acid position 113 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