chrX-55488483-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_201286.4(USP51):āc.457A>Gā(p.Arg153Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000758 in 1,186,879 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_201286.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USP51 | NM_201286.4 | c.457A>G | p.Arg153Gly | missense_variant | 3/3 | ENST00000500968.4 | |
USP51 | XM_017029300.2 | c.457A>G | p.Arg153Gly | missense_variant | 3/3 | ||
USP51 | XM_017029301.2 | c.457A>G | p.Arg153Gly | missense_variant | 2/2 | ||
USP51 | XM_047441870.1 | c.457A>G | p.Arg153Gly | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USP51 | ENST00000500968.4 | c.457A>G | p.Arg153Gly | missense_variant | 3/3 | 1 | NM_201286.4 | P1 | |
USP51 | ENST00000586165.1 | c.124+211A>G | intron_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.00000905 AC: 1AN: 110457Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33049
GnomAD3 exomes AF: 0.0000125 AC: 2AN: 160502Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 50712
GnomAD4 exome AF: 0.00000743 AC: 8AN: 1076422Hom.: 0 Cov.: 36 AF XY: 0.00000572 AC XY: 2AN XY: 349362
GnomAD4 genome AF: 0.00000905 AC: 1AN: 110457Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 33049
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 13, 2023 | The c.457A>G (p.R153G) alteration is located in exon 2 (coding exon 1) of the USP51 gene. This alteration results from a A to G substitution at nucleotide position 457, causing the arginine (R) at amino acid position 153 to be replaced by a glycine (G). 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