rs1147129

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_007347.5(AP4E1):c.222+18G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.551 in 1,603,050 control chromosomes in the GnomAD database, including 245,547 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.57 ( 24500 hom., cov: 33)

Exomes 𝑓: 0.55 ( 221047 hom. )

Consequence

AP4E1
NM_007347.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: 0.00700

Variant links:

Genes affected

AP4E1 (HGNC:573): (adaptor related protein complex 4 subunit epsilon 1) This gene encodes a member of the adaptor complexes large subunit protein family. These proteins are components of the heterotetrameric adaptor protein complexes, which play important roles in the secretory and endocytic pathways by mediating vesicle formation and sorting of integral membrane proteins. The encoded protein is a large subunit of adaptor protein complex-4, which is associated with both clathrin- and nonclathrin-coated vesicles. Disruption of this gene may be associated with cerebral palsy. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Nov 2011]

AP4E1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.61).

BP6

Variant 15-50912167-G-A is Benign according to our data. Variant chr15-50912167-G-A is described in ClinVar as [Benign]. Clinvar id is 380768.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr15-50912167-G-A is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AP4E1	NM_007347.5 linkuse as main transcript	c.222+18G>A		intron_variant		ENST00000261842.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AP4E1	ENST00000261842.10 linkuse as main transcript	c.222+18G>A		intron_variant		1	NM_007347.5	P1	Q9UPM8-1

Frequencies

GnomAD3 genomes

AF:

0.566

AC:

85913

AN:

151904

Hom.:

24490

Cov.:

show subpopulations

Gnomad AFR

AF:

0.606

Gnomad AMI

AF:

0.479

Gnomad AMR

AF:

0.613

Gnomad ASJ

AF:

0.654

Gnomad EAS

AF:

0.414

Gnomad SAS

AF:

0.618

Gnomad FIN

AF:

0.577

Gnomad MID

AF:

0.627

Gnomad NFE

AF:

0.533

Gnomad OTH

AF:

0.568

GnomAD3 exomes

AF:

0.570

AC:

143375

AN:

251352

Hom.:

41599

AF XY:

0.569

AC XY:

77298

AN XY:

135870

show subpopulations

Gnomad AFR exome

AF:

0.602

Gnomad AMR exome

AF:

0.672

Gnomad ASJ exome

AF:

0.649

Gnomad EAS exome

AF:

0.428

Gnomad SAS exome

AF:

0.609

Gnomad FIN exome

AF:

0.573

Gnomad NFE exome

AF:

0.540

Gnomad OTH exome

AF:

0.569

GnomAD4 exome

AF:

0.549

AC:

796634

AN:

1451028

Hom.:

221047

Cov.:

AF XY:

0.550

AC XY:

397446

AN XY:

722558

show subpopulations

Gnomad4 AFR exome

AF:

0.614

Gnomad4 AMR exome

AF:

0.663

Gnomad4 ASJ exome

AF:

0.657

Gnomad4 EAS exome

AF:

0.424

Gnomad4 SAS exome

AF:

0.611

Gnomad4 FIN exome

AF:

0.566

Gnomad4 NFE exome

AF:

0.538

Gnomad4 OTH exome

AF:

0.553

GnomAD4 genome

AF:

0.565

AC:

85962

AN:

152022

Hom.:

24500

Cov.:

AF XY:

0.568

AC XY:

42182

AN XY:

74302

show subpopulations

Gnomad4 AFR

AF:

0.606

Gnomad4 AMR

AF:

0.612

Gnomad4 ASJ

AF:

0.654

Gnomad4 EAS

AF:

0.413

Gnomad4 SAS

AF:

0.616

Gnomad4 FIN

AF:

0.577

Gnomad4 NFE

AF:

0.533

Gnomad4 OTH

AF:

0.569

Alfa

AF:

0.562

Hom.:

4945

Bravo

AF:

0.571

Asia WGS

AF:

0.521

AC:

1814

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Hereditary spastic paraplegia 51

Benign:3

Benign, criteria provided, single submitter	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	May 31, 2017	- -
Benign, no assertion criteria provided	clinical testing	Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	-	- -
Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 14, 2021	- -

Spastic paraplegia

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Feb 01, 2024

- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Feb 01, 2016

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.61

Cadd

Benign

Dann

Benign

0.79

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over