chr1-16294688-C-T

Variant names:

• chr1-16294688-C-T
• rs1007150
• NM_018994.3:c.502+95G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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. 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 NM_018994.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FBXO42	NM_018994.3	c.502+95G>A		intron_variant	Intron 4 of 9	ENST00000375592.8	NP_061867.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FBXO42	ENST00000375592.8	c.502+95G>A		intron_variant	Intron 4 of 9	1	NM_018994.3	ENSP00000364742.3
FBXO42	ENST00000478089.1	n.546G>A		non_coding_transcript_exon_variant	Exon 3 of 3	1

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

Gnomad4 AFR exome AF: 0.528

Gnomad4 AMR exome AF: 0.545

Gnomad4 ASJ exome AF: 0.656

Gnomad4 EAS exome AF: 0.865

Gnomad4 SAS exome AF: 0.554

Gnomad4 FIN exome AF: 0.839

Gnomad4 NFE exome AF: 0.765

Gnomad4 OTH exome AF: 0.724

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

Gnomad4 AFR AF: 0.534

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.656

Gnomad4 EAS AF: 0.861

Gnomad4 SAS AF: 0.559

Gnomad4 FIN AF: 0.849

Gnomad4 NFE AF: 0.763

Gnomad4 OTH AF: 0.665

Alfa AF: 0.735 Hom.: 41892

Bravo AF: 0.662

Asia WGS AF: 0.661 AC: 2300 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.25
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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

LitVar

Other links and lift over

dbSNP: rs1007150; hg19: chr1-16621183;