rs12255505
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001391956.1(USP54):c.2060+79G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 1,522,264 control chromosomes in the GnomAD database, including 15,384 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.19 ( 4971 hom., cov: 32)
Exomes 𝑓: 0.093 ( 10413 hom. )
Consequence
USP54
NM_001391956.1 intron
NM_001391956.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.716
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.89).
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
USP54 | NM_001391956.1 | c.2060+79G>T | intron_variant | ENST00000687698.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USP54 | ENST00000687698.1 | c.2060+79G>T | intron_variant | NM_001391956.1 | P3 |
Frequencies
GnomAD3 genomes ? AF: 0.188 AC: 28653AN: 152016Hom.: 4945 Cov.: 32
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GnomAD3 exomes AF: 0.134 AC: 32832AN: 245476Hom.: 3854 AF XY: 0.132 AC XY: 17615AN XY: 133510
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GnomAD4 exome AF: 0.0932 AC: 127761AN: 1370130Hom.: 10413 Cov.: 23 AF XY: 0.0960 AC XY: 65904AN XY: 686294
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GnomAD4 genome ? AF: 0.189 AC: 28734AN: 152134Hom.: 4971 Cov.: 32 AF XY: 0.189 AC XY: 14044AN XY: 74406
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at