chr16-28910488-T-C

Position:

• chr16-28910488-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.1089+400A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.752 in 158,204 control chromosomes in the GnomAD database, including 46,157 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 (44706 hom., cov: 29)
  • Exomes 𝑓: 0.66 (1451 hom.)
• Consequence: RABEP2 NM_024816.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

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=-0.91).
• 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.1089+400A>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.1089+400A>G		intron_variant		1	NM_024816.3	ENSP00000350934.4
RABEP2	ENST00000357573.10	c.993+400A>G		intron_variant		1		ENSP00000350186.6
RABEP2	ENST00000562590.5	n.2010A>G		non_coding_transcript_exon_variant	7/7	1
RABEP2	ENST00000544477.5	c.876+400A>G		intron_variant		2		ENSP00000442798.1

Frequencies

GnomAD3 genomes AF: 0.756 AC: 114625 AN: 151720 Hom.: 44656 Cov.: 29

Gnomad AFR AF: 0.938

Gnomad AMI AF: 0.802

Gnomad AMR AF: 0.641

Gnomad ASJ AF: 0.780

Gnomad EAS AF: 0.889

Gnomad SAS AF: 0.826

Gnomad FIN AF: 0.640

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.670

Gnomad OTH AF: 0.767

GnomAD4 exome AF: 0.664 AC: 4225 AN: 6366 Hom.: 1451 Cov.: 0 AF XY: 0.673 AC XY: 2231 AN XY: 3316

Gnomad4 AFR exome AF: 0.922

Gnomad4 AMR exome AF: 0.590

Gnomad4 ASJ exome AF: 0.746

Gnomad4 EAS exome AF: 0.876

Gnomad4 SAS exome AF: 0.792

Gnomad4 FIN exome AF: 0.564

Gnomad4 NFE exome AF: 0.642

Gnomad4 OTH exome AF: 0.677

GnomAD4 genome AF: 0.756 AC: 114723 AN: 151838 Hom.: 44706 Cov.: 29 AF XY: 0.755 AC XY: 56026 AN XY: 74188

Gnomad4 AFR AF: 0.938

Gnomad4 AMR AF: 0.640

Gnomad4 ASJ AF: 0.780

Gnomad4 EAS AF: 0.889

Gnomad4 SAS AF: 0.827

Gnomad4 FIN AF: 0.640

Gnomad4 NFE AF: 0.670

Gnomad4 OTH AF: 0.765

Alfa AF: 0.600 Hom.: 1879

Bravo AF: 0.762

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	-0.91
CADD	Benign	0.92
DANN	Benign	0.44

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: rs7184597; hg19: chr16-28921809;