1-16294688-C-T

Variant names:

• chr1-16294688-C-T
• rs1007150
• ENST00000478089.1:n.546G>A

Variant summary

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

The ENST00000478089.1(FBXO42):​n.546G>A variant causes a non coding transcript exon 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.68 (36485 hom., cov: 32)
  • Exomes 𝑓: 0.74 (336125 hom.)
• Consequence: FBXO42 ENST00000478089.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180
• Publications: 12 publications found

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]

ACMG classification

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: ENST00000478089.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.683 AC: 103748 AN: 151904 Hom.: 36470 Cov.: 32

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.: 15 AF XY: 0.739 AC XY: 440129 AN XY: 595540

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

GnomAD4 genome AF: 0.683 AC: 103800 AN: 152022 Hom.: 36485 Cov.: 32 AF XY: 0.682 AC XY: 50692 AN XY: 74320

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

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
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)

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

Other links and lift over

dbSNP: rs1007150; hg19: chr1-16621183;