Genetic Variant ENST00000392001.6:n.-338G>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 ENST00000452801.2(RAB17-DT):n.99+142C>T 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-DT
ENST00000452801.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.232

Publications

0 publications found

Variant links:

Genes affected

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

RAB17-DT links:

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:

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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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
RAB17-DT	NR_187201.1 link	n.108+142C>T	intron_variant	Intron 1 of 2
RAB17-DT	NR_187202.1 link	n.108+142C>T	intron_variant	Intron 1 of 1
RAB17-DT	NR_187203.1 link	n.108+142C>T	intron_variant	Intron 1 of 2
RAB17-DT	NR_187204.1 link	n.108+142C>T	intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
RAB17-DT	ENST00000452801.2 link	n.99+142C>T	intron_variant	Intron 1 of 2	2
RAB17-DT	ENST00000470375.2 link	n.248+142C>T	intron_variant	Intron 1 of 2	2
RAB17	ENST00000487008.1 link	n.109-435G>A	intron_variant	Intron 1 of 1	3

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 v4.3

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

Publications

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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