rs3132485
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000494673.1(USP8P1):n.41C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.429 in 457,708 control chromosomes in the GnomAD database, including 43,788 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 0.44 ( 14776 hom., cov: 32)
Exomes 𝑓: 0.42 ( 29012 hom. )
Consequence
USP8P1
ENST00000494673.1 non_coding_transcript_exon
ENST00000494673.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.246
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=-0.58).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
USP8P1 | ENST00000494673.1 | n.41C>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.440 AC: 66846AN: 151816Hom.: 14762 Cov.: 32
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GnomAD4 exome AF: 0.423 AC: 129431AN: 305772Hom.: 29012 Cov.: 0 AF XY: 0.414 AC XY: 68475AN XY: 165302
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GnomAD4 genome ? AF: 0.440 AC: 66888AN: 151936Hom.: 14776 Cov.: 32 AF XY: 0.435 AC XY: 32342AN XY: 74282
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at