dbSNP rs1007150: FBXO42:c.502+95G>A (chr1-16294688-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 NM_018994.3(FBXO42):c.502+95G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.737 in 1,350,434 control chromosomes in the GnomAD database, including 372,610 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as (no stars).

Frequency

Genomes: 𝑓 0.68 ( 36485 hom., cov: 32)

Exomes 𝑓: 0.74 ( 336125 hom. )

Consequence

FBXO42
NM_018994.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0180

Publications

12 publications found

Variant links:

Genes affected

FBXO42 (HGNC:29249): (F-box protein 42) Members of the F-box protein family, such as FBXO42, are characterized by an approximately 40-amino acid F-box motif. SCF complexes, formed by SKP1 (SKP1A; MIM 601434), cullin (see CUL1; MIM 603134), and F-box proteins, act as protein-ubiquitin ligases. F-box proteins interact with SKP1 through the F box, and they interact with ubiquitination targets through other protein interaction domains (Jin et al., 2004 [PubMed 15520277]).[supplied by OMIM, Dec 2010]

FBXO42 links:

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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 (EAS) allele frequency at 95% confidence interval = 0.84 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018994.3. 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
	FBXO42	NM_018994.3	MANE Select	c.502+95G>A		intron	N/A	NP_061867.1	Q6P3S6

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
FBXO42	ENST00000375592.8	TSL:1 MANE Select	c.502+95G>A	intron	N/A	ENSP00000364742.3	Q6P3S6
FBXO42	ENST00000478089.1	TSL:1	n.546G>A	non_coding_transcript_exon	Exon 3 of 3
FBXO42	ENST00000868586.1		c.502+95G>A	intron	N/A	ENSP00000538645.1

Frequencies

GnomAD3 genomes

AF:

0.683

AC:

103748

AN:

151904

Hom.:

36470

Cov.:

show subpopulations

Gnomad AFR

AF:

0.534

Gnomad AMI

AF:

0.709

Gnomad AMR

AF:

0.600

Gnomad ASJ

AF:

0.656

Gnomad EAS

AF:

0.860

Gnomad SAS

AF:

0.559

Gnomad FIN

AF:

0.849

Gnomad MID

AF:

0.601

Gnomad NFE

AF:

0.763

Gnomad OTH

AF:

0.670

GnomAD4 exome

AF:

0.744

AC:

892124

AN:

1198412

Hom.:

336125

Cov.:

AF XY:

0.739

AC XY:

440129

AN XY:

595540

show subpopulations

African (AFR)

AF:

0.528

AC:

14515

AN:

27488

American (AMR)

AF:

0.545

AC:

16222

AN:

29774

Ashkenazi Jewish (ASJ)

AF:

0.656

AC:

13005

AN:

19820

East Asian (EAS)

AF:

0.865

AC:

32569

AN:

37640

South Asian (SAS)

AF:

0.554

AC:

36668

AN:

66128

European-Finnish (FIN)

AF:

0.839

AC:

41754

AN:

49740

Middle Eastern (MID)

AF:

0.579

AC:

2890

AN:

4994

European-Non Finnish (NFE)

AF:

0.765

AC:

698048

AN:

912482

Other (OTH)

AF:

0.724

AC:

36453

AN:

50346

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

Heterozygous variant carriers

10486

20973

31459

41946

52432

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

16452

32904

49356

65808

82260

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.683

AC:

103800

AN:

152022

Hom.:

36485

Cov.:

AF XY:

0.682

AC XY:

50692

AN XY:

74320

show subpopulations

African (AFR)

AF:

0.534

AC:

22117

AN:

41434

American (AMR)

AF:

0.599

AC:

9134

AN:

15238

Ashkenazi Jewish (ASJ)

AF:

0.656

AC:

2275

AN:

3468

East Asian (EAS)

AF:

0.861

AC:

4460

AN:

5182

South Asian (SAS)

AF:

0.559

AC:

2695

AN:

4820

European-Finnish (FIN)

AF:

0.849

AC:

8992

AN:

10586

Middle Eastern (MID)

AF:

0.605

AC:

178

AN:

294

European-Non Finnish (NFE)

AF:

0.763

AC:

51901

AN:

67980

Other (OTH)

AF:

0.665

AC:

1404

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1622

3244

4867

6489

8111

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

808

1616

2424

3232

4040

<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:

0.724

Hom.:

59559

Bravo

AF:

0.662

Asia WGS

AF:

0.661

AC:

2300

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

1.3

(source)

DANN

Benign

0.25

PhyloP100

-0.018

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over