Variant rs1131095 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001640.4(APEH):c.852T>C(p.Tyr284Tyr) 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: 𝑓 0.27 ( 6246 hom., cov: 33)

Exomes 𝑓: 0.29 ( 62965 hom. )

Consequence

APEH
NM_001640.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.18

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:

APEH (HGNC:):

APEH links:

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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 linkuse as main transcript	c.852T>C	p.Tyr284Tyr	synonymous_variant	9/22	ENST00000296456.10	NP_001631.3	P13798

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
APEH	ENST00000296456.10 linkuse as main transcript	c.852T>C	p.Tyr284Tyr	synonymous_variant	9/22	1	NM_001640.4	ENSP00000296456.5		P13798

Frequencies

GnomAD3 genomes

AF:

0.275

AC:

41764

AN:

152112

Hom.:

6242

Cov.:

show subpopulations

Gnomad AFR

AF:

0.251

Gnomad AMI

AF:

0.196

Gnomad AMR

AF:

0.207

Gnomad ASJ

AF:

0.442

Gnomad EAS

AF:

0.0459

Gnomad SAS

AF:

0.216

Gnomad FIN

AF:

0.447

Gnomad MID

AF:

0.313

Gnomad NFE

AF:

0.291

Gnomad OTH

AF:

0.286

GnomAD3 exomes

AF:

0.265

AC:

66732

AN:

251442

Hom.:

10363

AF XY:

0.269

AC XY:

36503

AN XY:

135894

show subpopulations

Gnomad AFR exome

AF:

0.248

Gnomad AMR exome

AF:

0.150

Gnomad ASJ exome

AF:

0.441

Gnomad EAS exome

AF:

0.0451

Gnomad SAS exome

AF:

0.228

Gnomad FIN exome

AF:

0.442

Gnomad NFE exome

AF:

0.298

Gnomad OTH exome

AF:

0.290

GnomAD4 exome

AF:

0.285

AC:

416806

AN:

1461842

Hom.:

62965

Cov.:

AF XY:

0.284

AC XY:

206601

AN XY:

727240

show subpopulations

Gnomad4 AFR exome

AF:

0.251

Gnomad4 AMR exome

AF:

0.157

Gnomad4 ASJ exome

AF:

0.440

Gnomad4 EAS exome

AF:

0.0436

Gnomad4 SAS exome

AF:

0.234

Gnomad4 FIN exome

AF:

0.431

Gnomad4 NFE exome

AF:

0.293

Gnomad4 OTH exome

AF:

0.288

GnomAD4 genome

AF:

0.275

AC:

41788

AN:

152230

Hom.:

6246

Cov.:

AF XY:

0.277

AC XY:

20583

AN XY:

74408

show subpopulations

Gnomad4 AFR

AF:

0.251

Gnomad4 AMR

AF:

0.206

Gnomad4 ASJ

AF:

0.442

Gnomad4 EAS

AF:

0.0460

Gnomad4 SAS

AF:

0.216

Gnomad4 FIN

AF:

0.447

Gnomad4 NFE

AF:

0.291

Gnomad4 OTH

AF:

0.284

Alfa

AF:

0.292

Hom.:

8716

Bravo

AF:

0.255

Asia WGS

AF:

0.131

AC:

461

AN:

3478

EpiCase

AF:

0.302

EpiControl

AF:

0.297

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.23

DANN

Benign

0.42

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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