12-62384284-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1
The NM_001252078.2(USP15):āc.1455A>Gā(p.Pro485Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.611 in 1,605,158 control chromosomes in the GnomAD database, including 300,818 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_001252078.2 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
USP15 | ENST00000280377.10 | c.1455A>G | p.Pro485Pro | synonymous_variant | Exon 11 of 22 | 1 | NM_001252078.2 | ENSP00000280377.5 | ||
USP15 | ENST00000353364.7 | c.1368A>G | p.Pro456Pro | synonymous_variant | Exon 10 of 21 | 1 | ENSP00000258123.4 | |||
USP15 | ENST00000549268.1 | n.813A>G | non_coding_transcript_exon_variant | Exon 4 of 7 | 5 |
Frequencies
GnomAD3 genomes AF: 0.594 AC: 87854AN: 147968Hom.: 26311 Cov.: 25
GnomAD3 exomes AF: 0.604 AC: 149724AN: 248070Hom.: 45516 AF XY: 0.600 AC XY: 80553AN XY: 134254
GnomAD4 exome AF: 0.613 AC: 892510AN: 1457116Hom.: 274501 Cov.: 37 AF XY: 0.610 AC XY: 442302AN XY: 724848
GnomAD4 genome AF: 0.594 AC: 87874AN: 148042Hom.: 26317 Cov.: 25 AF XY: 0.595 AC XY: 42912AN XY: 72066
ClinVar
Submissions by phenotype
USP15-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at