rs1131095
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The ENST00000296456.10(APEH):āc.852T>Cā(p.Tyr284=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 1,614,072 control chromosomes in the GnomAD database, including 69,211 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: š 0.27 ( 6246 hom., cov: 33)
Exomes š: 0.29 ( 62965 hom. )
Consequence
APEH
ENST00000296456.10 synonymous
ENST00000296456.10 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.18
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 -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP7
Synonymous conserved (PhyloP=-1.18 with no splicing effect.
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
APEH | NM_001640.4 | c.852T>C | p.Tyr284= | synonymous_variant | 9/22 | ENST00000296456.10 | NP_001631.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
APEH | ENST00000296456.10 | c.852T>C | p.Tyr284= | synonymous_variant | 9/22 | 1 | NM_001640.4 | ENSP00000296456 | P1 |
Frequencies
GnomAD3 genomes AF: 0.275 AC: 41764AN: 152112Hom.: 6242 Cov.: 33
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GnomAD3 exomes AF: 0.265 AC: 66732AN: 251442Hom.: 10363 AF XY: 0.269 AC XY: 36503AN XY: 135894
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GnomAD4 exome AF: 0.285 AC: 416806AN: 1461842Hom.: 62965 Cov.: 64 AF XY: 0.284 AC XY: 206601AN XY: 727240
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GnomAD4 genome AF: 0.275 AC: 41788AN: 152230Hom.: 6246 Cov.: 33 AF XY: 0.277 AC XY: 20583AN XY: 74408
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Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at