Variant rs9822268 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

Scores

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]

APEH links:

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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 linkuse as main transcript	c.1604-52G>A		intron_variant		ENST00000296456.10	NP_001631.3	P13798

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
APEH	ENST00000296456.10 linkuse as main transcript	c.1604-52G>A	intron_variant	1	NM_001640.4	ENSP00000296456.5	P13798
APEH	ENST00000438011.5 linkuse as main transcript	c.1604-52G>A	intron_variant	1		ENSP00000415862.1	C9JIF9
APEH	ENST00000469362.6 linkuse as main transcript	n.*304-52G>A	intron_variant	3		ENSP00000438180.1	H0YFE5

Frequencies

GnomAD3 genomes

AF:

0.280

AC:

42647

AN:

152102

Hom.:

6460

Cov.:

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.:

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.:

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over