dbSNP rs2275075: RAB25:c.*232A>C (chr1-156070519-A-C) – 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 NM_020387.4(RAB25):c.*232A>C variant causes a downstream gene 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: 30)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

RAB25
NM_020387.4 downstream_gene

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0260

Publications

13 publications found

Variant links:

Genes affected

RAB25 (HGNC:18238): (RAB25, member RAS oncogene family) The protein encoded by this gene is a member of the RAS superfamily of small GTPases. The encoded protein is involved in membrane trafficking and cell survival. This gene has been found to be a tumor suppressor and an oncogene, depending on the context. Two variants, one protein-coding and the other not, have been found for this gene. [provided by RefSeq, Nov 2015]

RAB25 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=-0.8).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RAB25	NM_020387.4 link	c.*232A>C		downstream_gene_variant		ENST00000361084.10	NP_065120.2	P57735
RAB25	NR_133653.2 link	n.*15A>C		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
RAB25	ENST00000361084.10 link	c.*232A>C	downstream_gene_variant	1	NM_020387.4	ENSP00000354376.5	P57735
RAB25	ENST00000497968.1 link	n.*154A>C	downstream_gene_variant	1
RAB25	ENST00000473336.5 link	n.*15A>C	downstream_gene_variant	2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

377804

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

197388

African (AFR)

AF:

0.00

AC:

AN:

10562

American (AMR)

AF:

0.00

AC:

AN:

13414

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

11088

East Asian (EAS)

AF:

0.00

AC:

AN:

24404

South Asian (SAS)

AF:

0.00

AC:

AN:

37918

European-Finnish (FIN)

AF:

0.00

AC:

AN:

21964

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1596

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

235380

Other (OTH)

AF:

0.00

AC:

AN:

21478

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

131051

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

7.8

(source)

DANN

Benign

0.75

PhyloP100

-0.026

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