16-2141733-A-G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000565592.5. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RAB26	ENST00000565592.5	TSL:1	n.-4+784A>G		intron	N/A	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

African (AFR) AF: 0.521 AC: 21568 AN: 41394

American (AMR) AF: 0.789 AC: 12035 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.746 AC: 2587 AN: 3470

East Asian (EAS) AF: 0.998 AC: 5179 AN: 5188

South Asian (SAS) AF: 0.925 AC: 4462 AN: 4826

European-Finnish (FIN) AF: 0.825 AC: 8668 AN: 10504

Middle Eastern (MID) AF: 0.716 AC: 209 AN: 292

European-Non Finnish (NFE) AF: 0.820 AC: 55754 AN: 67964

Other (OTH) AF: 0.742 AC: 1564 AN: 2108

Alfa AF: 0.795 Hom.: 56386

Bravo AF: 0.730

Asia WGS AF: 0.923 AC: 3209 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.6
DANN	Benign	0.60
PhyloP100		0.0080

Splicing

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

Other links and lift over

dbSNP: rs258281; hg19: chr16-2191734;