rs11825259

Variant names:

• chr11-33785276-A-G
• rs11825259
• ENST00000718487.1:n.417+8936A>G

Your query was ambiguous. Multiple possible variants found:

• chr11-33785276-A-G
• chr11-33785276-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000718487.1(FBXO3-DT):​n.417+8936A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0321 in 152,188 control chromosomes in the GnomAD database, including 258 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 0.032 (258 hom., cov: 31)
• Consequence: FBXO3-DT ENST00000718487.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.445
• Publications: 5 publications found

Genes affected

FBXO3-DT (HGNC:51147): (FBXO3 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.105 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000718487.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FBXO3-DT	ENST00000718487.1		n.417+8936A>G		intron	N/A
	FBXO3-DT	ENST00000718488.1		n.365-1867A>G		intron	N/A
	FBXO3-DT	ENST00000718489.1		n.364+8936A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0321 AC: 4875 AN: 152070 Hom.: 258 Cov.: 31

Gnomad AFR AF: 0.108

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0111

Gnomad ASJ AF: 0.00259

Gnomad EAS AF: 0.00289

Gnomad SAS AF: 0.0244

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000779

Gnomad OTH AF: 0.0273

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

GnomAD4 genome AF: 0.0321 AC: 4883 AN: 152188 Hom.: 258 Cov.: 31 AF XY: 0.0310 AC XY: 2310 AN XY: 74424

African (AFR) AF: 0.108 AC: 4464 AN: 41514

American (AMR) AF: 0.0110 AC: 168 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.00259 AC: 9 AN: 3472

East Asian (EAS) AF: 0.00309 AC: 16 AN: 5180

South Asian (SAS) AF: 0.0240 AC: 116 AN: 4824

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10570

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.000779 AC: 53 AN: 68020

Other (OTH) AF: 0.0270 AC: 57 AN: 2108

Alfa AF: 0.00933 Hom.: 9

Bravo AF: 0.0364

Asia WGS AF: 0.0130 AC: 46 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.6
DANN	Benign	0.62
PhyloP100		0.45

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11825259;

hg19: chr11-33806822;