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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0930
Variant links:
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]

Genome browser will be placed here

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
APEHNM_001640.4 linkuse as main transcriptc.1604-52G>A intron_variant ENST00000296456.10 NP_001631.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
APEHENST00000296456.10 linkuse as main transcriptc.1604-52G>A intron_variant 1 NM_001640.4 ENSP00000296456 P1
APEHENST00000438011.5 linkuse as main transcriptc.1604-52G>A intron_variant 1 ENSP00000415862
APEHENST00000469362.6 linkuse as main transcriptc.*304-52G>A intron_variant, NMD_transcript_variant 3 ENSP00000438180

Frequencies

GnomAD3 genomes
AF:
0.280
AC:
42647
AN:
152102
Hom.:
6460
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.272
Gnomad AMI
AF:
0.196
Gnomad AMR
AF:
0.208
Gnomad ASJ
AF:
0.443
Gnomad EAS
AF:
0.0454
Gnomad SAS
AF:
0.216
Gnomad FIN
AF:
0.448
Gnomad MID
AF:
0.320
Gnomad NFE
AF:
0.291
Gnomad OTH
AF:
0.288
GnomAD4 exome
AF:
0.286
AC:
388941
AN:
1361944
Hom.:
58996
Cov.:
25
AF XY:
0.284
AC XY:
193032
AN XY:
678846
show subpopulations
Gnomad4 AFR exome
AF:
0.274
Gnomad4 AMR exome
AF:
0.161
Gnomad4 ASJ exome
AF:
0.441
Gnomad4 EAS exome
AF:
0.0428
Gnomad4 SAS exome
AF:
0.234
Gnomad4 FIN exome
AF:
0.432
Gnomad4 NFE exome
AF:
0.292
Gnomad4 OTH exome
AF:
0.289
GnomAD4 genome
AF:
0.280
AC:
42675
AN:
152218
Hom.:
6464
Cov.:
34
AF XY:
0.282
AC XY:
20993
AN XY:
74406
show subpopulations
Gnomad4 AFR
AF:
0.272
Gnomad4 AMR
AF:
0.208
Gnomad4 ASJ
AF:
0.443
Gnomad4 EAS
AF:
0.0455
Gnomad4 SAS
AF:
0.216
Gnomad4 FIN
AF:
0.448
Gnomad4 NFE
AF:
0.291
Gnomad4 OTH
AF:
0.286
Alfa
AF:
0.265
Hom.:
4311
Bravo
AF:
0.262
Asia WGS
AF:
0.135
AC:
474
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
1.8
DANN
Benign
0.76
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.1

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs9822268; hg19: chr3-49719729; COSMIC: COSV56532731; COSMIC: COSV56532731; API