chr5-108067237-C-T

Variant names:

• chr5-108067237-C-T
• rs286751
• NM_001163315.3:c.1746-46236G>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.1746-46236G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.632 in 151,864 control chromosomes in the GnomAD database, including 30,845 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 0.63 (30845 hom., cov: 31)
• Consequence: FBXL17 NM_001163315.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00
• Publications: 4 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=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.812 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.1746-46236G>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.1746-46236G>A		intron	N/A	ENSP00000437464.2
	FBXL17	ENST00000496714.2	TSL:1	c.753-46236G>A		intron	N/A	ENSP00000418111.2
	FBXL17	ENST00000481160.1	TSL:3	n.402-46236G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.632 AC: 95848 AN: 151744 Hom.: 30793 Cov.: 31

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.376

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.768

Gnomad SAS AF: 0.835

Gnomad FIN AF: 0.620

Gnomad MID AF: 0.580

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.623

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

GnomAD4 genome AF: 0.632 AC: 95961 AN: 151864 Hom.: 30845 Cov.: 31 AF XY: 0.638 AC XY: 47351 AN XY: 74224

African (AFR) AF: 0.717 AC: 29677 AN: 41406

American (AMR) AF: 0.591 AC: 9014 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.648 AC: 2244 AN: 3464

East Asian (EAS) AF: 0.768 AC: 3976 AN: 5174

South Asian (SAS) AF: 0.834 AC: 4015 AN: 4816

European-Finnish (FIN) AF: 0.620 AC: 6532 AN: 10534

Middle Eastern (MID) AF: 0.583 AC: 169 AN: 290

European-Non Finnish (NFE) AF: 0.570 AC: 38676 AN: 67902

Other (OTH) AF: 0.625 AC: 1315 AN: 2104

Alfa AF: 0.591 Hom.: 34339

Bravo AF: 0.631

Asia WGS AF: 0.790 AC: 2742 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.15
DANN	Benign	0.78
PhyloP100		-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: rs286751; hg19: chr5-107402938; COSMIC: COSV62860349;