rs72795980

Variant names:

• chr5-107946648-C-T
• rs72795980
• NM_001163315.3:c.1823-65469G>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.1823-65469G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 151,514 control chromosomes in the GnomAD database, including 2,251 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 0.17 (2251 hom., cov: 28)
• Consequence: FBXL17 NM_001163315.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.644
• Publications: 1 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.21 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.1823-65469G>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.1823-65469G>A		intron	N/A	ENSP00000437464.2
	FBXL17	ENST00000496714.2	TSL:1	c.830-65469G>A		intron	N/A	ENSP00000418111.2

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25222 AN: 151408 Hom.: 2240 Cov.: 28

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.0396

Gnomad AMR AF: 0.108

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.0342

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.178

Gnomad MID AF: 0.173

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.167 AC: 25268 AN: 151514 Hom.: 2251 Cov.: 28 AF XY: 0.167 AC XY: 12369 AN XY: 73990

African (AFR) AF: 0.214 AC: 8836 AN: 41274

American (AMR) AF: 0.108 AC: 1646 AN: 15218

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 577 AN: 3470

East Asian (EAS) AF: 0.0343 AC: 176 AN: 5134

South Asian (SAS) AF: 0.196 AC: 939 AN: 4792

European-Finnish (FIN) AF: 0.178 AC: 1861 AN: 10458

Middle Eastern (MID) AF: 0.176 AC: 51 AN: 290

European-Non Finnish (NFE) AF: 0.159 AC: 10789 AN: 67864

Other (OTH) AF: 0.170 AC: 357 AN: 2106

Alfa AF: 0.165 Hom.: 469

Bravo AF: 0.162

Asia WGS AF: 0.117 AC: 407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.36
DANN	Benign	0.24
PhyloP100		-0.64
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: rs72795980; hg19: chr5-107282349;