chr5-107912907-C-T

Variant names:

• chr5-107912907-C-T
• rs1433050
• NM_001163315.3:c.1823-31728G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001163315.3. 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
	FBXL17	NM_001163315.3	MANE Select	c.1823-31728G>A		intron	N/A	NP_001156787.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FBXL17	ENST00000542267.7	TSL:1 MANE Select	c.1823-31728G>A		intron	N/A	ENSP00000437464.2
	FBXL17	ENST00000496714.2	TSL:1	c.830-31728G>A		intron	N/A	ENSP00000418111.2

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

African (AFR) AF: 0.826 AC: 34243 AN: 41474

American (AMR) AF: 0.807 AC: 12321 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.847 AC: 2942 AN: 3472

East Asian (EAS) AF: 0.479 AC: 2468 AN: 5148

South Asian (SAS) AF: 0.746 AC: 3593 AN: 4816

European-Finnish (FIN) AF: 0.797 AC: 8434 AN: 10580

Middle Eastern (MID) AF: 0.806 AC: 237 AN: 294

European-Non Finnish (NFE) AF: 0.795 AC: 54047 AN: 67968

Other (OTH) AF: 0.810 AC: 1713 AN: 2114

Alfa AF: 0.792 Hom.: 202603

Bravo AF: 0.796

Asia WGS AF: 0.662 AC: 2303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.9
DANN	Benign	0.76
PhyloP100		0.53
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: rs1433050; hg19: chr5-107248608;