rs10520818

Positions:

• chr5-15589808-G-A

Variant summary

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

The NM_012304.5(FBXL7):​c.38-26175G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.14 in 152,076 control chromosomes in the GnomAD database, including 1,560 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 0.14 (1560 hom., cov: 31)
• Consequence: FBXL7 NM_012304.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.609

Genes affected

FBXL7 (HGNC:13604): (F-box and leucine rich repeat protein 7) This gene encodes a member of the F-box protein family which is characterized by a 42-48 amino acid motif, the F-box, which binds to the S-phase kinase-associated protein 1 (Skp1) protein. The F-box proteins constitute one of the four subunits of E3 ubiquitin protein ligases called SCFs (SKP1-Cul1-F-box), which play a role in phosphorylation-dependent ubiquitination of proteins. The F-box proteins are divided into 3 subfamilies based on the other domain in the protein: F-box proteins that also have a WD-40 domain (Fbws subfamily), F-box proteins that also have leucine-rich repeats (Fbls subfamily) and F-box proteins that contain other motifs or lack known protein-interaction domains (Fbxs subfamily). The protein encoded by this gene belongs to the Fbls subfamily. Alternative splicing results in multiple transcript variants of this gene. [provided by RefSeq, May 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FBXL7	NM_012304.5	c.38-26175G>A		intron_variant		ENST00000504595.2
FBXL7	NM_001278317.2	c.-104-26175G>A		intron_variant
FBXL7	XM_017009262.3	c.22+8996G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FBXL7	ENST00000504595.2	c.38-26175G>A		intron_variant		1	NM_012304.5	P1
FBXL7	ENST00000510662.1	c.-104-26175G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21265 AN: 151958 Hom.: 1556 Cov.: 31

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.139

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.145

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.140 AC: 21282 AN: 152076 Hom.: 1560 Cov.: 31 AF XY: 0.144 AC XY: 10671 AN XY: 74322

Gnomad4 AFR AF: 0.166

Gnomad4 AMR AF: 0.139

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.145

Gnomad4 SAS AF: 0.232

Gnomad4 FIN AF: 0.159

Gnomad4 NFE AF: 0.116

Gnomad4 OTH AF: 0.126

Alfa AF: 0.126 Hom.: 746

Bravo AF: 0.137

Asia WGS AF: 0.193 AC: 672 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.70
DANN	Benign	0.44

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: rs10520818; hg19: chr5-15589917;