NM_024816.3:c.1089+400A>G

Variant names:

• chr16-28910488-T-C
• rs7184597
• NM_024816.3:c.1089+400A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 30 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024816.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RABEP2	NM_024816.3	MANE Select	c.1089+400A>G		intron	N/A	NP_079092.2	Q9H5N1-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RABEP2	ENST00000358201.9	TSL:1 MANE Select	c.1089+400A>G		intron	N/A	ENSP00000350934.4	Q9H5N1-1
	RABEP2	ENST00000357573.10	TSL:1	c.993+400A>G		intron	N/A	ENSP00000350186.6	Q9H5N1-2
	RABEP2	ENST00000562590.5	TSL:1	n.2010A>G		non_coding_transcript_exon	Exon 7 of 7

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

African (AFR) AF: 0.922 AC: 142 AN: 154

American (AMR) AF: 0.590 AC: 522 AN: 884

Ashkenazi Jewish (ASJ) AF: 0.746 AC: 97 AN: 130

East Asian (EAS) AF: 0.876 AC: 170 AN: 194

South Asian (SAS) AF: 0.792 AC: 404 AN: 510

European-Finnish (FIN) AF: 0.564 AC: 97 AN: 172

Middle Eastern (MID) AF: 0.917 AC: 22 AN: 24

European-Non Finnish (NFE) AF: 0.642 AC: 2553 AN: 3976

Other (OTH) AF: 0.677 AC: 218 AN: 322

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

African (AFR) AF: 0.938 AC: 38888 AN: 41444

American (AMR) AF: 0.640 AC: 9728 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.780 AC: 2705 AN: 3466

East Asian (EAS) AF: 0.889 AC: 4586 AN: 5158

South Asian (SAS) AF: 0.827 AC: 3974 AN: 4808

European-Finnish (FIN) AF: 0.640 AC: 6749 AN: 10552

Middle Eastern (MID) AF: 0.820 AC: 241 AN: 294

European-Non Finnish (NFE) AF: 0.670 AC: 45515 AN: 67900

Other (OTH) AF: 0.765 AC: 1607 AN: 2100

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.92
DANN	Benign	0.44
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7184597; hg19: chr16-28921809;