rs9822268
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000296456.10(APEH):c.1604-52G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 1,514,162 control chromosomes in the GnomAD database, including 65,460 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 0.28 ( 6464 hom., cov: 34)
Exomes 𝑓: 0.29 ( 58996 hom. )
Consequence
APEH
ENST00000296456.10 intron
ENST00000296456.10 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0930
Genes affected
APEH (HGNC:586): (acylaminoacyl-peptide hydrolase) This gene encodes the enzyme acylpeptide hydrolase, which catalyzes the hydrolysis of the terminal acetylated amino acid preferentially from small acetylated peptides. The acetyl amino acid formed by this hydrolase is further processed to acetate and a free amino acid by an aminoacylase. This gene is located within the same region of chromosome 3 (3p21) as the aminoacylase gene, and deletions at this locus are also associated with a decrease in aminoacylase activity. The acylpeptide hydrolase is a homotetrameric protein of 300 kDa with each subunit consisting of 732 amino acid residues. It can play an important role in destroying oxidatively damaged proteins in living cells. Deletions of this gene locus are found in various types of carcinomas, including small cell lung carcinoma and renal cell carcinoma. [provided by RefSeq, Jul 2008]
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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=-0.82).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.287 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
APEH | NM_001640.4 | c.1604-52G>A | intron_variant | ENST00000296456.10 | NP_001631.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
APEH | ENST00000296456.10 | c.1604-52G>A | intron_variant | 1 | NM_001640.4 | ENSP00000296456 | P1 | |||
APEH | ENST00000438011.5 | c.1604-52G>A | intron_variant | 1 | ENSP00000415862 | |||||
APEH | ENST00000469362.6 | c.*304-52G>A | intron_variant, NMD_transcript_variant | 3 | ENSP00000438180 |
Frequencies
GnomAD3 genomes AF: 0.280 AC: 42647AN: 152102Hom.: 6460 Cov.: 34
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GnomAD4 exome AF: 0.286 AC: 388941AN: 1361944Hom.: 58996 Cov.: 25 AF XY: 0.284 AC XY: 193032AN XY: 678846
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GnomAD4 genome AF: 0.280 AC: 42675AN: 152218Hom.: 6464 Cov.: 34 AF XY: 0.282 AC XY: 20993AN 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
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at