NM_001640.4:c.1604-52G>A
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001640.4(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
NM_001640.4 intron
NM_001640.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0930
Publications
59 publications found
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 was made for transcript
Our verdict: Benign. The variant received -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
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
APEH | ENST00000296456.10 | c.1604-52G>A | intron_variant | Intron 17 of 21 | 1 | NM_001640.4 | ENSP00000296456.5 | |||
APEH | ENST00000438011.5 | c.1604-52G>A | intron_variant | Intron 17 of 21 | 1 | ENSP00000415862.1 | ||||
APEH | ENST00000469362.6 | n.*304-52G>A | intron_variant | Intron 6 of 8 | 3 | ENSP00000438180.1 |
Frequencies
GnomAD3 genomes AF: 0.280 AC: 42647AN: 152102Hom.: 6460 Cov.: 34 show subpopulations
GnomAD3 genomes
AF:
AC:
42647
AN:
152102
Hom.:
Cov.:
34
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.286 AC: 388941AN: 1361944Hom.: 58996 Cov.: 25 AF XY: 0.284 AC XY: 193032AN XY: 678846 show subpopulations
GnomAD4 exome
AF:
AC:
388941
AN:
1361944
Hom.:
Cov.:
25
AF XY:
AC XY:
193032
AN XY:
678846
show subpopulations
African (AFR)
AF:
AC:
8495
AN:
31014
American (AMR)
AF:
AC:
6593
AN:
41068
Ashkenazi Jewish (ASJ)
AF:
AC:
11159
AN:
25282
East Asian (EAS)
AF:
AC:
1608
AN:
37550
South Asian (SAS)
AF:
AC:
19171
AN:
82006
European-Finnish (FIN)
AF:
AC:
22431
AN:
51906
Middle Eastern (MID)
AF:
AC:
1696
AN:
5584
European-Non Finnish (NFE)
AF:
AC:
301374
AN:
1030712
Other (OTH)
AF:
AC:
16414
AN:
56822
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
14253
28507
42760
57014
71267
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
9642
19284
28926
38568
48210
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.280 AC: 42675AN: 152218Hom.: 6464 Cov.: 34 AF XY: 0.282 AC XY: 20993AN XY: 74406 show subpopulations
GnomAD4 genome
AF:
AC:
42675
AN:
152218
Hom.:
Cov.:
34
AF XY:
AC XY:
20993
AN XY:
74406
show subpopulations
African (AFR)
AF:
AC:
11293
AN:
41524
American (AMR)
AF:
AC:
3176
AN:
15302
Ashkenazi Jewish (ASJ)
AF:
AC:
1537
AN:
3472
East Asian (EAS)
AF:
AC:
236
AN:
5186
South Asian (SAS)
AF:
AC:
1043
AN:
4830
European-Finnish (FIN)
AF:
AC:
4743
AN:
10588
Middle Eastern (MID)
AF:
AC:
92
AN:
294
European-Non Finnish (NFE)
AF:
AC:
19772
AN:
67998
Other (OTH)
AF:
AC:
605
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1636
3272
4907
6543
8179
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
434
868
1302
1736
2170
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
474
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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