16-67225760-C-T

Variant names:

• chr16-67225760-C-T
• rs7196989
• ENST00000409509.5:n.36+1215G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000409509.5(FBXL9P):​n.36+1215G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,092 control chromosomes in the GnomAD database, including 8,871 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 0.23 (8871 hom., cov: 32)
• Consequence: FBXL9P ENST00000409509.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710
• Publications: 9 publications found

Genes affected

FBXL9P (HGNC:):

FBXL9P (HGNC:13605): (F-box and leucine rich repeat protein, pseudogene) This gene encodes a member of the F-box protein family which is characterized by an approximately 40 amino acid motif, the F-box. The F-box proteins constitute one of the four subunits of ubiquitin protein ligase complex called SCFs (SKP1-cullin-F-box), which function in phosphorylation-dependent ubiquitination. The F-box proteins are divided into 3 classes: Fbws containing WD-40 domains, Fbls containing leucine-rich repeats, and Fbxs containing either different protein-protein interaction modules or no recognizable motifs. The protein encoded by this gene belongs to the Fbls class and, in addition to an F-box, contains 9 tandem leucine-rich repeats. Two transcript variants encoding the same protein have been found for this gene. Other variants may occur, but their full-length natures have not been characterized. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.626 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000409509.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FBXL9P	NR_172488.1		n.51+1215G>A		intron	N/A
	FBXL9P	NR_172489.1		n.173+870G>A		intron	N/A
	FBXL9P	NR_172490.1		n.173+870G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FBXL9P	ENST00000409509.5	TSL:1	n.36+1215G>A		intron	N/A
	FBXL9P	ENST00000637247.2	TSL:1	n.237+870G>A		intron	N/A
	FBXL9P	ENST00000409037.6	TSL:5	n.42+1215G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35331 AN: 151974 Hom.: 8832 Cov.: 32

Gnomad AFR AF: 0.632

Gnomad AMI AF: 0.113

Gnomad AMR AF: 0.120

Gnomad ASJ AF: 0.0340

Gnomad EAS AF: 0.0212

Gnomad SAS AF: 0.165

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0676

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.233 AC: 35431 AN: 152092 Hom.: 8871 Cov.: 32 AF XY: 0.231 AC XY: 17200 AN XY: 74360

African (AFR) AF: 0.632 AC: 26205 AN: 41432

American (AMR) AF: 0.120 AC: 1830 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0340 AC: 118 AN: 3470

East Asian (EAS) AF: 0.0213 AC: 110 AN: 5174

South Asian (SAS) AF: 0.164 AC: 793 AN: 4826

European-Finnish (FIN) AF: 0.122 AC: 1290 AN: 10588

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0676 AC: 4596 AN: 67990

Other (OTH) AF: 0.169 AC: 357 AN: 2114

Alfa AF: 0.110 Hom.: 1198

Bravo AF: 0.247

Asia WGS AF: 0.148 AC: 516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.36
PhyloP100		-0.071
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: rs7196989; hg19: chr16-67259663;