chr11-33802952-T-G

Variant names:

• chr11-33802952-T-G
• rs1533800
• ENST00000718487.1:n.418-1965T>G

Variant summary

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

The ENST00000718487.1(FBXO3-DT):​n.418-1965T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 152,048 control chromosomes in the GnomAD database, including 30,024 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 0.62 (30024 hom., cov: 32)
• Consequence: FBXO3-DT ENST00000718487.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.895
• Publications: 4 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=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.686 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.418-1965T>G		intron	N/A
	FBXO3-DT	ENST00000718488.1		n.757-1965T>G		intron	N/A
	FBXO3-DT	ENST00000718489.1		n.365-1965T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.621 AC: 94309 AN: 151930 Hom.: 30033 Cov.: 32

Gnomad AFR AF: 0.488

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.679

Gnomad ASJ AF: 0.799

Gnomad EAS AF: 0.603

Gnomad SAS AF: 0.706

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.674

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.620 AC: 94323 AN: 152048 Hom.: 30024 Cov.: 32 AF XY: 0.619 AC XY: 46013 AN XY: 74292

African (AFR) AF: 0.487 AC: 20217 AN: 41480

American (AMR) AF: 0.679 AC: 10377 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.799 AC: 2770 AN: 3466

East Asian (EAS) AF: 0.602 AC: 3107 AN: 5162

South Asian (SAS) AF: 0.705 AC: 3401 AN: 4822

European-Finnish (FIN) AF: 0.605 AC: 6385 AN: 10552

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.674 AC: 45819 AN: 67962

Other (OTH) AF: 0.663 AC: 1396 AN: 2106

Alfa AF: 0.648 Hom.: 6753

Bravo AF: 0.623

Asia WGS AF: 0.596 AC: 2072 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	3.1
DANN	Benign	0.86
PhyloP100		-0.90

Splicing

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

Other links and lift over

dbSNP: rs1533800; hg19: chr11-33824498;