Genetic Variant FBXL9P:n.36+1215G>A (chr16-67225760-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000409509.5(FBXL9P):n.36+1215G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,092 control chromosomes in the GnomAD database, including 8,871 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 0.23 ( 8871 hom., cov: 32)

Consequence

FBXL9P
ENST00000409509.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0710

Publications

9 publications found

Variant links:

Genes affected

FBXL9P (HGNC:):

FBXL9P links:

FBXL9P (HGNC:13605): (F-box and leucine rich repeat protein, pseudogene) This gene encodes a member of the F-box protein family which is characterized by an approximately 40 amino acid motif, the F-box. The F-box proteins constitute one of the four subunits of ubiquitin protein ligase complex called SCFs (SKP1-cullin-F-box), which function in phosphorylation-dependent ubiquitination. The F-box proteins are divided into 3 classes: Fbws containing WD-40 domains, Fbls containing leucine-rich repeats, and Fbxs containing either different protein-protein interaction modules or no recognizable motifs. The protein encoded by this gene belongs to the Fbls class and, in addition to an F-box, contains 9 tandem leucine-rich repeats. Two transcript variants encoding the same protein have been found for this gene. Other variants may occur, but their full-length natures have not been characterized. [provided by RefSeq, Jul 2008]

FBXL9P links:

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new If you want to explore the variant's impact on the transcript ENST00000409509.5, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000409509.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
FBXL9P	NR_172488.1	n.51+1215G>A	intron	N/A
FBXL9P	NR_172489.1	n.173+870G>A	intron	N/A
FBXL9P	NR_172490.1	n.173+870G>A	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
FBXL9P	ENST00000409509.5	TSL:1	n.36+1215G>A	intron	N/A
FBXL9P	ENST00000637247.2	TSL:1	n.237+870G>A	intron	N/A
FBXL9P	ENST00000409037.6	TSL:5	n.42+1215G>A	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.232

AC:

35331

AN:

151974

Hom.:

8832

Cov.:

show subpopulations

Gnomad AFR

AF:

0.632

Gnomad AMI

AF:

0.113

Gnomad AMR

AF:

0.120

Gnomad ASJ

AF:

0.0340

Gnomad EAS

AF:

0.0212

Gnomad SAS

AF:

0.165

Gnomad FIN

AF:

0.122

Gnomad MID

AF:

0.0949

Gnomad NFE

AF:

0.0676

Gnomad OTH

AF:

0.169

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

GnomAD4 genome

AF:

0.233

AC:

35431

AN:

152092

Hom.:

8871

Cov.:

AF XY:

0.231

AC XY:

17200

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.632

AC:

26205

AN:

41432

American (AMR)

AF:

0.120

AC:

1830

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.0340

AC:

118

AN:

3470

East Asian (EAS)

AF:

0.0213

AC:

110

AN:

5174

South Asian (SAS)

AF:

0.164

AC:

793

AN:

4826

European-Finnish (FIN)

AF:

0.122

AC:

1290

AN:

10588

Middle Eastern (MID)

AF:

0.0986

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0676

AC:

4596

AN:

67990

Other (OTH)

AF:

0.169

AC:

357

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

914

1828

2741

3655

4569

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

302

604

906

1208

1510

<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:

0.110

Hom.:

1198

Bravo

AF:

0.247

Asia WGS

AF:

0.148

AC:

516

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.8

(source)

DANN

Benign

0.36

PhyloP100

-0.071

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over