5-107912907-C-T

Position:

• chr5-107912907-C-T

Variant summary

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

The NM_001163315.3(FBXL17):​c.1823-31728G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.794 in 152,054 control chromosomes in the GnomAD database, including 48,375 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 0.79 (48375 hom., cov: 31)
• Consequence: FBXL17 NM_001163315.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.527

Genes affected

FBXL17 (HGNC:13615): (F-box and leucine rich repeat protein 17) Members of the F-box protein family, such as FBXL17, are characterized by an approximately 40-amino acid F-box motif. SCF complexes, formed by SKP1 (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, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.818 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FBXL17	NM_001163315.3	c.1823-31728G>A		intron_variant		ENST00000542267.7
FBXL17	XM_005272048.5	c.1823-31728G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FBXL17	ENST00000542267.7	c.1823-31728G>A		intron_variant		1	NM_001163315.3	P1
FBXL17	ENST00000496714.2	c.831-31728G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.794 AC: 120695 AN: 151936 Hom.: 48323 Cov.: 31

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.884

Gnomad AMR AF: 0.807

Gnomad ASJ AF: 0.847

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.745

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.795

Gnomad OTH AF: 0.815

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

GnomAD4 genome AF: 0.794 AC: 120804 AN: 152054 Hom.: 48375 Cov.: 31 AF XY: 0.792 AC XY: 58872 AN XY: 74306

Gnomad4 AFR AF: 0.826

Gnomad4 AMR AF: 0.807

Gnomad4 ASJ AF: 0.847

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.746

Gnomad4 FIN AF: 0.797

Gnomad4 NFE AF: 0.795

Gnomad4 OTH AF: 0.810

Alfa AF: 0.794 Hom.: 98747

Bravo AF: 0.796

Asia WGS AF: 0.662 AC: 2303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.9
DANN	Benign	0.76

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: rs1433050; hg19: chr5-107248608;