dbSNP rs1533800: FBXO3-DT:n.418-1965T>G (chr11-33802952-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.895

Publications

4 publications found

Variant links:

Genes affected

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

FBXO3-DT links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
FBXO3-DT	ENST00000718487.1 link	n.418-1965T>G	intron_variant	Intron 3 of 8
FBXO3-DT	ENST00000718488.1 link	n.757-1965T>G	intron_variant	Intron 6 of 8
FBXO3-DT	ENST00000718489.1 link	n.365-1965T>G	intron_variant	Intron 3 of 8

Frequencies

GnomAD3 genomes

AF:

0.621

AC:

94309

AN:

151930

Hom.:

30033

Cov.:

show subpopulations

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.:

AF XY:

0.619

AC XY:

46013

AN XY:

74292

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1756

3511

5267

7022

8778

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

778

1556

2334

3112

3890

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

3.1

(source)

DANN

Benign

0.86

PhyloP100

-0.90

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over