11-119359250-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_004205.5(USP2):c.1042C>T(p.Pro348Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000075 in 1,613,972 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P348L) has been classified as Uncertain significance.
Frequency
Consequence
NM_004205.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USP2 | NM_004205.5 | c.1042C>T | p.Pro348Ser | missense_variant | 5/13 | ENST00000260187.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USP2 | ENST00000260187.7 | c.1042C>T | p.Pro348Ser | missense_variant | 5/13 | 1 | NM_004205.5 | ||
USP2-AS1 | ENST00000706409.1 | n.251+2533G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.000171 AC: 26AN: 152112Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000597 AC: 15AN: 251338Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135878
GnomAD4 exome AF: 0.0000643 AC: 94AN: 1461742Hom.: 0 Cov.: 32 AF XY: 0.0000509 AC XY: 37AN XY: 727168
GnomAD4 genome AF: 0.000177 AC: 27AN: 152230Hom.: 0 Cov.: 32 AF XY: 0.000228 AC XY: 17AN XY: 74432
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 06, 2023 | The c.1042C>T (p.P348S) alteration is located in exon 5 (coding exon 4) of the USP2 gene. This alteration results from a C to T substitution at nucleotide position 1042, causing the proline (P) at amino acid position 348 to be replaced by a serine (S). 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