Genetic Variant FBXL18:c.*1226dupA (chr7-5480548-A-AT) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is . The variant received -4 ACMG points: 0P and 4B. BS2

The NM_024963.6(FBXL18):c.*1226dupA variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00057 ( 2 hom., cov: 0)

Failed GnomAD Quality Control

Consequence

FBXL18
NM_024963.6 3_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.827

Publications

0 publications found

Variant links:

Genes affected

FBXL18 (HGNC:21874): (F-box and leucine rich repeat protein 18) The protein encoded by this gene is a member of a family of proteins that contain an approximately 40-amino acid F-box motif. This motif is important for interaction with SKP1 and for targeting some proteins for degradation. The encoded protein has been shown to control the cellular level of FBXL7, a protein that induces mitotic arrest, by targeting it for polyubiquitylation and proteasomal degradation. Members of the F-box protein family, such as FBXL18, are characterized by an approximately 40-amino acid F-box motif. F-box proteins interact with SKP1 through the F box, and they interact with ubiquitination targets through other protein interaction domains. [provided by RefSeq, Mar 2016]

FBXL18 links:

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new If you want to explore the variant's impact on the transcript NM_024963.6, 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: Likely_benign. The variant received -4 ACMG points.

BS2

High Homozygotes in GnomAd4 at 2 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024963.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
FBXL18	NM_024963.6	MANE Select	c.*1226dupA	3_prime_UTR	Exon 5 of 5	NP_079239.3
FBXL18	NM_001367780.1		c.*1226dupA	3_prime_UTR	Exon 5 of 5	NP_001354709.1
FBXL18	NM_001367781.1		c.*1226dupA	3_prime_UTR	Exon 5 of 5	NP_001354710.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FBXL18	ENST00000382368.8	TSL:5 MANE Select	c.*1226dupA	3_prime_UTR	Exon 5 of 5	ENSP00000371805.3	Q96ME1-4
FBXL18	ENST00000948868.1		c.*1226dupA	splice_region	Exon 4 of 4	ENSP00000618927.1
FBXL18	ENST00000948868.1		c.*1226dupA	3_prime_UTR	Exon 4 of 4	ENSP00000618927.1

Frequencies

GnomAD3 genomes

AF:

0.000570

AC:

AN:

40346

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000481

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000746

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000539

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000710

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AC0;AS_VQSR

AC:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.000570

AC:

AN:

40336

Hom.:

Cov.:

AF XY:

0.000389

AC XY:

AN XY:

18014

show subpopulations

African (AFR)

AF:

0.000480

AC:

AN:

10420

American (AMR)

AF:

0.000746

AC:

AN:

2680

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

1290

East Asian (EAS)

AF:

0.000541

AC:

AN:

1848

South Asian (SAS)

AF:

0.00

AC:

AN:

1162

European-Finnish (FIN)

AF:

0.00

AC:

AN:

926

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.000710

AC:

AN:

21124

Other (OTH)

AF:

0.00

AC:

AN:

542

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.441

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<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:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.83

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.

Publications

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7-5480548-ATTTTTTTTTTTTTTTTTTT-ATTTTTTTTTTTTTTTTTTTT

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