Genetic Variant RAB17:c.-364-435G>A (chr2-237591409-C-T) – 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 ENST00000904315.1(RAB17):c.-364-435G>A variant causes a intron 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: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

RAB17
ENST00000904315.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.232

Publications

0 publications found

Variant links:

Genes affected

RAB17 (HGNC:16523): (RAB17, member RAS oncogene family) The Rab subfamily of small GTPases plays an important role in the regulation of membrane trafficking. RAB17 is an epithelial cell-specific GTPase (Lutcke et al., 1993 [PubMed 8486736]).[supplied by OMIM, Oct 2009]

RAB17 links:

RAB17-DT (HGNC:56028): (RAB17 divergent transcript)

RAB17-DT links:

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new If you want to explore the variant's impact on the transcript ENST00000904315.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.7).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000904315.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
RAB17-DT	NR_187201.1	n.108+142C>T	intron	N/A
RAB17-DT	NR_187202.1	n.108+142C>T	intron	N/A
RAB17-DT	NR_187203.1	n.108+142C>T	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
RAB17	ENST00000904315.1		c.-364-435G>A	intron	N/A	ENSP00000574374.1
RAB17-DT	ENST00000452801.2	TSL:2	n.99+142C>T	intron	N/A
RAB17-DT	ENST00000470375.2	TSL:2	n.248+142C>T	intron	N/A

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

114700

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

61450

African (AFR)

AF:

0.00

AC:

AN:

824

American (AMR)

AF:

0.00

AC:

AN:

3766

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2768

East Asian (EAS)

AF:

0.00

AC:

AN:

1908

South Asian (SAS)

AF:

0.00

AC:

AN:

19920

European-Finnish (FIN)

AF:

0.00

AC:

AN:

20428

Middle Eastern (MID)

AF:

0.00

AC:

AN:

828

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

58866

Other (OTH)

AF:

0.00

AC:

AN:

5392

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

Bravo

AF:

0.00000756

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.70

CADD

Benign

5.1

(source)

DANN

Benign

0.74

PhyloP100

0.23

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over