16-28914657-T-C

Position:

• chr16-28914657-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_024816.3(RABEP2):​c.543+15A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.695 in 1,613,346 control chromosomes in the GnomAD database, including 395,782 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 0.76 (44771 hom., cov: 32)
  • Exomes 𝑓: 0.69 (351011 hom.)
• Consequence: RABEP2 NM_024816.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

Genes affected

RABEP2 (HGNC:24817): (rabaptin, RAB GTPase binding effector protein 2) Predicted to enable GTPase activator activity and growth factor activity. Involved in regulation of cilium assembly. Located in cytosol; intracellular membrane-bounded organelle; and microtubule organizing center. [provided by Alliance of Genome Resources, Apr 2022]

RABEP2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.931 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RABEP2	NM_024816.3	c.543+15A>G		intron_variant		ENST00000358201.9	NP_079092.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RABEP2	ENST00000358201.9	c.543+15A>G		intron_variant		1	NM_024816.3	ENSP00000350934.4

Frequencies

GnomAD3 genomes AF: 0.755 AC: 114817 AN: 151990 Hom.: 44722 Cov.: 32

Gnomad AFR AF: 0.938

Gnomad AMI AF: 0.802

Gnomad AMR AF: 0.638

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.827

Gnomad FIN AF: 0.642

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.671

Gnomad OTH AF: 0.765

GnomAD3 exomes AF: 0.708 AC: 176070 AN: 248806 Hom.: 64203 AF XY: 0.715 AC XY: 96504 AN XY: 135008

Gnomad AFR exome AF: 0.944

Gnomad AMR exome AF: 0.537

Gnomad ASJ exome AF: 0.762

Gnomad EAS exome AF: 0.900

Gnomad SAS exome AF: 0.820

Gnomad FIN exome AF: 0.638

Gnomad NFE exome AF: 0.675

Gnomad OTH exome AF: 0.699

GnomAD4 exome AF: 0.689 AC: 1006731 AN: 1461240 Hom.: 351011 Cov.: 44 AF XY: 0.693 AC XY: 503552 AN XY: 726952

Gnomad4 AFR exome AF: 0.953

Gnomad4 AMR exome AF: 0.539

Gnomad4 ASJ exome AF: 0.766

Gnomad4 EAS exome AF: 0.874

Gnomad4 SAS exome AF: 0.818

Gnomad4 FIN exome AF: 0.638

Gnomad4 NFE exome AF: 0.669

Gnomad4 OTH exome AF: 0.719

GnomAD4 genome AF: 0.755 AC: 114914 AN: 152106 Hom.: 44771 Cov.: 32 AF XY: 0.755 AC XY: 56127 AN XY: 74338

Gnomad4 AFR AF: 0.938

Gnomad4 AMR AF: 0.637

Gnomad4 ASJ AF: 0.767

Gnomad4 EAS AF: 0.885

Gnomad4 SAS AF: 0.827

Gnomad4 FIN AF: 0.642

Gnomad4 NFE AF: 0.671

Gnomad4 OTH AF: 0.763

Alfa AF: 0.634 Hom.: 3377

Bravo AF: 0.761

Asia WGS AF: 0.798 AC: 2778 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.016
DANN	Benign	0.33
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs3924376; hg19: chr16-28925978;