rs12113318

Positions:

• chr7-103043980-T-G

Variant summary

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

The ENST00000440067.4(FBXL13):​c.270+11108A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 152,192 control chromosomes in the GnomAD database, including 1,790 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 0.15 (1790 hom., cov: 32)
• Consequence: FBXL13 ENST00000440067.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16

Genes affected

FBXL13 (HGNC:21658): (F-box and leucine rich repeat protein 13) Members of the F-box protein family, such as FBXL13, 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.21 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FBXL13	NM_001394494.2	c.270+11108A>C		intron_variant		ENST00000440067.4
FBXL13	NR_105043.2	n.296+11108A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FBXL13	ENST00000440067.4	c.270+11108A>C		intron_variant		3	NM_001394494.2	P2

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22102 AN: 152074 Hom.: 1783 Cov.: 32

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.143

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0829

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.148

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

GnomAD4 genome AF: 0.145 AC: 22126 AN: 152192 Hom.: 1790 Cov.: 32 AF XY: 0.142 AC XY: 10530 AN XY: 74408

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.116

Gnomad4 ASJ AF: 0.143

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.0829

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.147

Alfa AF: 0.135 Hom.: 3069

Bravo AF: 0.149

Asia WGS AF: 0.0600 AC: 212 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	11
DANN	Benign	0.54

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: rs12113318; hg19: chr7-102684427;