rs2275075

Variant names:

• chr1-156070519-A-C
• rs2275075
• NM_020387.4:c.*232A>C

Your query was ambiguous. Multiple possible variants found:

• chr1-156070519-A-C
• chr1-156070519-A-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000361084.10(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 ENST00000361084.10 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0260
• Publications: 13 publications found

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]

ACMG classification

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).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000361084.10. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RAB25	NM_020387.4	MANE Select	c.*232A>C		downstream_gene	N/A	NP_065120.2
	RAB25	NR_133653.2		n.*15A>C		downstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RAB25	ENST00000361084.10	TSL:1 MANE Select	c.*232A>C		downstream_gene	N/A	ENSP00000354376.5
	RAB25	ENST00000497968.1	TSL:1	n.*154A>C		downstream_gene	N/A
	RAB25	ENST00000473336.5	TSL:2	n.*15A>C		downstream_gene	N/A

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 377804 Hom.: 0 Cov.: 5 AF XY: 0.00 AC XY: 0 AN XY: 197388

African (AFR) AF: 0.00 AC: 0 AN: 10562

American (AMR) AF: 0.00 AC: 0 AN: 13414

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11088

East Asian (EAS) AF: 0.00 AC: 0 AN: 24404

South Asian (SAS) AF: 0.00 AC: 0 AN: 37918

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 21964

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1596

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 235380

Other (OTH) AF: 0.00 AC: 0 AN: 21478

GnomAD4 genome Cov.: 30

Alfa AF: 0.00 Hom.: 131051

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.8
DANN	Benign	0.75
PhyloP100		-0.026

Splicing

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

Other links and lift over

dbSNP: rs2275075; hg19: chr1-156040310;