Variant chr17-5381475-G-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_004703.6(RABEP1):c.2457G>A(p.Arg819=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 1,610,816 control chromosomes in the GnomAD database, including 187,492 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 0.52 ( 21594 hom., cov: 32)

Exomes 𝑓: 0.46 ( 165898 hom. )

Consequence

RABEP1
NM_004703.6 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.461

Variant links:

Genes affected

RABEP1 (HGNC:17677): (rabaptin, RAB GTPase binding effector protein 1) Enables protein domain specific binding activity and protein homodimerization activity. Involved in vesicle-mediated transport. Located in endocytic vesicle and endosome. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

RABEP1 links:

NUP88 (HGNC:8067): (nucleoporin 88) The nuclear pore complex is a massive structure that extends across the nuclear envelope, forming a gateway that regulates the flow of macromolecules between the nucleus and the cytoplasm. Nucleoporins, a family of 50 to 100 proteins, are the main components of the nuclear pore complex in eukaryotic cells. The protein encoded by this gene belongs to the nucleoporin family and is associated with the oncogenic nucleoporin CAN/Nup214 in a dynamic subcomplex. This protein is also overexpressed in a large number of malignant neoplasms and precancerous dysplasias. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Mar 2016]

NUP88 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=-0.52).

BP7

Synonymous conserved (PhyloP=0.461 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.945 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RABEP1	NM_004703.6 linkuse as main transcript	c.2457G>A	p.Arg819=	synonymous_variant	17/18	ENST00000537505.6	NP_004694.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RABEP1	ENST00000537505.6 linkuse as main transcript	c.2457G>A	p.Arg819=	synonymous_variant	17/18	1	NM_004703.6	ENSP00000445408	P1	Q15276-1

Frequencies

GnomAD3 genomes

AF:

0.515

AC:

78234

AN:

151900

Hom.:

21554

Cov.:

show subpopulations

Gnomad AFR

AF:

0.607

Gnomad AMI

AF:

0.245

Gnomad AMR

AF:

0.482

Gnomad ASJ

AF:

0.403

Gnomad EAS

AF:

0.968

Gnomad SAS

AF:

0.745

Gnomad FIN

AF:

0.604

Gnomad MID

AF:

0.491

Gnomad NFE

AF:

0.412

Gnomad OTH

AF:

0.493

GnomAD3 exomes

AF:

0.533

AC:

132450

AN:

248518

Hom.:

38952

AF XY:

0.535

AC XY:

72103

AN XY:

134804

show subpopulations

Gnomad AFR exome

AF:

0.612

Gnomad AMR exome

AF:

0.506

Gnomad ASJ exome

AF:

0.410

Gnomad EAS exome

AF:

0.972

Gnomad SAS exome

AF:

0.733

Gnomad FIN exome

AF:

0.597

Gnomad NFE exome

AF:

0.408

Gnomad OTH exome

AF:

0.493

GnomAD4 exome

AF:

0.460

AC:

670737

AN:

1458798

Hom.:

165898

Cov.:

AF XY:

0.467

AC XY:

338614

AN XY:

725640

show subpopulations

Gnomad4 AFR exome

AF:

0.610

Gnomad4 AMR exome

AF:

0.506

Gnomad4 ASJ exome

AF:

0.401

Gnomad4 EAS exome

AF:

0.978

Gnomad4 SAS exome

AF:

0.722

Gnomad4 FIN exome

AF:

0.578

Gnomad4 NFE exome

AF:

0.408

Gnomad4 OTH exome

AF:

0.491

GnomAD4 genome

AF:

0.515

AC:

78337

AN:

152018

Hom.:

21594

Cov.:

AF XY:

0.531

AC XY:

39429

AN XY:

74312

show subpopulations

Gnomad4 AFR

AF:

0.608

Gnomad4 AMR

AF:

0.482

Gnomad4 ASJ

AF:

0.403

Gnomad4 EAS

AF:

0.968

Gnomad4 SAS

AF:

0.743

Gnomad4 FIN

AF:

0.604

Gnomad4 NFE

AF:

0.412

Gnomad4 OTH

AF:

0.498

Alfa

AF:

0.433

Hom.:

24402

Bravo

AF:

0.508

Asia WGS

AF:

0.835

AC:

2898

AN:

3478

EpiCase

AF:

0.410

EpiControl

AF:

0.410

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.52

CADD

Benign

5.5

DANN

Benign

0.78

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over