chr11-119357807-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004205.5(USP2):c.1451G>A(p.Arg484Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000031 in 1,613,960 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004205.5 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 |
---|---|---|---|---|---|---|---|
USP2 | NM_004205.5 | c.1451G>A | p.Arg484Gln | missense_variant | 10/13 | ENST00000260187.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USP2 | ENST00000260187.7 | c.1451G>A | p.Arg484Gln | missense_variant | 10/13 | 1 | NM_004205.5 | ||
USP2 | ENST00000525735.1 | c.824G>A | p.Arg275Gln | missense_variant | 9/12 | 1 | P1 | ||
USP2 | ENST00000455332.6 | c.722G>A | p.Arg241Gln | missense_variant | 9/12 | 1 | |||
USP2-AS1 | ENST00000706409.1 | n.251+1090C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152118Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251262Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135858
GnomAD4 exome AF: 0.0000322 AC: 47AN: 1461724Hom.: 0 Cov.: 37 AF XY: 0.0000330 AC XY: 24AN XY: 727150
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152236Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74420
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at