chr17-5381385-T-C

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The NM_004703.6(RABEP1):​c.2371-4T>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0114 in 1,605,954 control chromosomes in the GnomAD database, including 106 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0085 ( 11 hom., cov: 33)
Exomes 𝑓: 0.012 ( 95 hom. )

Consequence

RABEP1
NM_004703.6 splice_region, intron

Scores

2
Splicing: ADA: 0.0002646
2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -0.0370
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]
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BP6
Variant 17-5381385-T-C is Benign according to our data. Variant chr17-5381385-T-C is described in ClinVar as [Benign]. Clinvar id is 771203.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS2
High Homozygotes in GnomAd4 at 11 gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RABEP1NM_004703.6 linkc.2371-4T>C splice_region_variant, intron_variant Intron 16 of 17 ENST00000537505.6 NP_004694.2 Q15276-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RABEP1ENST00000537505.6 linkc.2371-4T>C splice_region_variant, intron_variant Intron 16 of 17 1 NM_004703.6 ENSP00000445408.2 Q15276-1

Frequencies

GnomAD3 genomes
AF:
0.00850
AC:
1294
AN:
152226
Hom.:
11
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00183
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00524
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00228
Gnomad FIN
AF:
0.0121
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0144
Gnomad OTH
AF:
0.0100
GnomAD3 exomes
AF:
0.00843
AC:
2032
AN:
240972
Hom.:
13
AF XY:
0.00838
AC XY:
1095
AN XY:
130636
show subpopulations
Gnomad AFR exome
AF:
0.00130
Gnomad AMR exome
AF:
0.00518
Gnomad ASJ exome
AF:
0.00105
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00192
Gnomad FIN exome
AF:
0.0140
Gnomad NFE exome
AF:
0.0129
Gnomad OTH exome
AF:
0.00874
GnomAD4 exome
AF:
0.0117
AC:
17008
AN:
1453610
Hom.:
95
Cov.:
29
AF XY:
0.0115
AC XY:
8279
AN XY:
722692
show subpopulations
Gnomad4 AFR exome
AF:
0.00124
Gnomad4 AMR exome
AF:
0.00490
Gnomad4 ASJ exome
AF:
0.000855
Gnomad4 EAS exome
AF:
0.0000253
Gnomad4 SAS exome
AF:
0.00230
Gnomad4 FIN exome
AF:
0.0146
Gnomad4 NFE exome
AF:
0.0137
Gnomad4 OTH exome
AF:
0.00929
GnomAD4 genome
AF:
0.00849
AC:
1294
AN:
152344
Hom.:
11
Cov.:
33
AF XY:
0.00803
AC XY:
598
AN XY:
74500
show subpopulations
Gnomad4 AFR
AF:
0.00183
Gnomad4 AMR
AF:
0.00523
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00228
Gnomad4 FIN
AF:
0.0121
Gnomad4 NFE
AF:
0.0144
Gnomad4 OTH
AF:
0.00992
Alfa
AF:
0.0109
Hom.:
5
Bravo
AF:
0.00785
Asia WGS
AF:
0.00173
AC:
6
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:3
-
Breakthrough Genomics, Breakthrough Genomics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: not provided

- -

Sep 01, 2024
CeGaT Center for Human Genetics Tuebingen
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

RABEP1: BP4, BS1, BS2 -

Oct 17, 2017
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.50
CADD
Benign
7.9
DANN
Benign
0.80

Splicing

Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
0.00026
dbscSNV1_RF
Benign
0.020
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.

Other links and lift over

dbSNP: rs112097489; hg19: chr17-5284680; API