rs258281

Variant names:

• chr16-2141733-A-G
• rs258281
• ENST00000565592.5:n.-4+784A>G

Your query was ambiguous. Multiple possible variants found:

• chr16-2141733-A-G
• chr16-2141733-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000565592.5(RAB26):​n.-4+784A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.742 in 151,914 control chromosomes in the GnomAD database, including 43,561 homozygotes. 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: 𝑓 0.74 (43561 hom., cov: 30)
• Consequence: RAB26 ENST00000565592.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800

Genes affected

RAB26 (HGNC:14259): (RAB26, member RAS oncogene family) Members of the RAB protein family, including RAB26, are important regulators of vesicular fusion and trafficking. The RAB family of small G proteins regulates intercellular vesicle trafficking, including exocytosis, endocytosis, and recycling (summary by Seki et al., 2000 [PubMed 11043516]).[supplied by OMIM, Nov 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RAB26	ENST00000565592.5	n.-4+784A>G		intron_variant	Intron 1 of 6	1		ENSP00000454373.1

Frequencies

GnomAD3 genomes AF: 0.743 AC: 112742 AN: 151796 Hom.: 43543 Cov.: 30

Gnomad AFR AF: 0.521

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.789

Gnomad ASJ AF: 0.746

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.924

Gnomad FIN AF: 0.825

Gnomad MID AF: 0.720

Gnomad NFE AF: 0.820

Gnomad OTH AF: 0.739

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.742 AC: 112790 AN: 151914 Hom.: 43561 Cov.: 30 AF XY: 0.747 AC XY: 55452 AN XY: 74250

Gnomad4 AFR AF: 0.521

Gnomad4 AMR AF: 0.789

Gnomad4 ASJ AF: 0.746

Gnomad4 EAS AF: 0.998

Gnomad4 SAS AF: 0.925

Gnomad4 FIN AF: 0.825

Gnomad4 NFE AF: 0.820

Gnomad4 OTH AF: 0.742

Alfa AF: 0.795 Hom.: 34659

Bravo AF: 0.730

Asia WGS AF: 0.923 AC: 3209 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.6
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs258281; hg19: chr16-2191734;