dbSNP rs7184597: RABEP2:n.2010A>T (chr16-28910488-T-A) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000562590.5(RABEP2):n.2010A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 29)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

RABEP2
ENST00000562590.5 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.08

Publications

30 publications found

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RABEP2	NM_024816.3 link	c.1089+400A>T		intron_variant	Intron 7 of 12	ENST00000358201.9	NP_079092.2	Q9H5N1-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
RABEP2	ENST00000562590.5 link	n.2010A>T	non_coding_transcript_exon_variant	Exon 7 of 7	1
RABEP2	ENST00000358201.9 link	c.1089+400A>T	intron_variant	Intron 7 of 12	1	NM_024816.3	ENSP00000350934.4	Q9H5N1-1
RABEP2	ENST00000357573.10 link	c.993+400A>T	intron_variant	Intron 6 of 10	1		ENSP00000350186.6	Q9H5N1-2
RABEP2	ENST00000544477.5 link	c.876+400A>T	intron_variant	Intron 6 of 11	2		ENSP00000442798.1	B4DHR0

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

6382

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

3328

African (AFR)

AF:

0.00

AC:

AN:

154

American (AMR)

AF:

0.00

AC:

AN:

886

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

130

East Asian (EAS)

AF:

0.00

AC:

AN:

194

South Asian (SAS)

AF:

0.00

AC:

AN:

510

European-Finnish (FIN)

AF:

0.00

AC:

AN:

172

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

3990

Other (OTH)

AF:

0.00

AC:

AN:

322

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

1879

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.78

(source)

DANN

Benign

0.44

PhyloP100

-1.1

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over