rs1058381

Positions:

• chr17-5384698-G-A
• chr17-5384698-G-C
• chr17-5384698-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_004703.6(RABEP1):​c.*1475G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.438 in 212,076 control chromosomes in the GnomAD database, including 21,902 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 0.44 (15149 hom., cov: 32)
  • Exomes 𝑓: 0.44 (6753 hom.)
• Consequence: RABEP1 NM_004703.6 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.760

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]

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.33).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RABEP1	NM_004703.6	c.*1475G>A		3_prime_UTR_variant	18/18	ENST00000537505.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RABEP1	ENST00000537505.6	c.*1475G>A		3_prime_UTR_variant	18/18	1	NM_004703.6	P1

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66070 AN: 151844 Hom.: 15140 Cov.: 32

Gnomad AFR AF: 0.414

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.389

Gnomad EAS AF: 0.837

Gnomad SAS AF: 0.642

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.427

GnomAD4 exome AF: 0.444 AC: 26669 AN: 60114 Hom.: 6753 Cov.: 0 AF XY: 0.446 AC XY: 12414 AN XY: 27836

Gnomad4 AFR exome AF: 0.395

Gnomad4 AMR exome AF: 0.374

Gnomad4 ASJ exome AF: 0.362

Gnomad4 EAS exome AF: 0.835

Gnomad4 SAS exome AF: 0.624

Gnomad4 FIN exome AF: 0.476

Gnomad4 NFE exome AF: 0.371

Gnomad4 OTH exome AF: 0.408

GnomAD4 genome AF: 0.435 AC: 66123 AN: 151962 Hom.: 15149 Cov.: 32 AF XY: 0.451 AC XY: 33467 AN XY: 74268

Gnomad4 AFR AF: 0.414

Gnomad4 AMR AF: 0.413

Gnomad4 ASJ AF: 0.389

Gnomad4 EAS AF: 0.837

Gnomad4 SAS AF: 0.641

Gnomad4 FIN AF: 0.588

Gnomad4 NFE AF: 0.390

Gnomad4 OTH AF: 0.433

Alfa AF: 0.383 Hom.: 10932

Bravo AF: 0.419

Asia WGS AF: 0.746 AC: 2589 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.33
CADD	Benign	12
DANN	Benign	0.89

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

Other links and lift over

dbSNP: rs1058381; hg19: chr17-5288018;