rs4486110

Positions:

• chr7-103017295-A-G
• chr7-103017295-A-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000440067.4(FBXL13):​c.765+7768T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.30 (7177 hom., cov: 28)
  • Failed GnomAD Quality Control
• Consequence: FBXL13 ENST00000440067.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118

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 Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FBXL13	NM_001394494.2	c.765+7768T>C		intron_variant		ENST00000440067.4	NP_001381423.1
FBXL13	NR_105043.2	n.791+7768T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FBXL13	ENST00000440067.4	c.765+7768T>C		intron_variant		3	NM_001394494.2	ENSP00000390126	P2

Frequencies

GnomAD3 genomes AF: 0.00 AC: 44219 AN: 145688 Hom.: 7158 Cov.: 28 FAILED QC

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.351

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.263

Gnomad EAS AF: 0.580

Gnomad SAS AF: 0.426

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.292

Gnomad OTH AF: 0.273

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.304 AC: 44272 AN: 145804 Hom.: 7177 Cov.: 28 AF XY: 0.304 AC XY: 21558 AN XY: 70910

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.291

Gnomad4 ASJ AF: 0.263

Gnomad4 EAS AF: 0.580

Gnomad4 SAS AF: 0.424

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.292

Gnomad4 OTH AF: 0.280

Alfa AF: 0.310 Hom.: 823

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	3.4
DANN	Benign	0.26

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: rs4486110; hg19: chr7-102657742;