rs983889

Variant names:

• chr5-15555377-G-T
• rs983889
• NM_012304.5:c.37+54664G>T

Variant summary

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

The NM_012304.5(FBXL7):​c.37+54664G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 152,032 control chromosomes in the GnomAD database, including 23,744 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 0.55 (23744 hom., cov: 32)
• Consequence: FBXL7 NM_012304.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261

Genes affected

FBXL7 (HGNC:13604): (F-box and leucine rich repeat protein 7) This gene encodes a member of the F-box protein family which is characterized by a 42-48 amino acid motif, the F-box, which binds to the S-phase kinase-associated protein 1 (Skp1) protein. The F-box proteins constitute one of the four subunits of E3 ubiquitin protein ligases called SCFs (SKP1-Cul1-F-box), which play a role in phosphorylation-dependent ubiquitination of proteins. The F-box proteins are divided into 3 subfamilies based on the other domain in the protein: F-box proteins that also have a WD-40 domain (Fbws subfamily), F-box proteins that also have leucine-rich repeats (Fbls subfamily) and F-box proteins that contain other motifs or lack known protein-interaction domains (Fbxs subfamily). The protein encoded by this gene belongs to the Fbls subfamily. Alternative splicing results in multiple transcript variants of this gene. [provided by RefSeq, May 2013]

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 = 0.713 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
FBXL7	NM_012304.5	c.37+54664G>T		intron_variant	Intron 1 of 3	ENST00000504595.2	NP_036436.1
FBXL7	NM_001278317.2	c.-105+53654G>T		intron_variant	Intron 1 of 3		NP_001265246.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
FBXL7	ENST00000504595.2	c.37+54664G>T		intron_variant	Intron 1 of 3	1	NM_012304.5	ENSP00000423630.1
FBXL7	ENST00000510662.1	c.-105+53654G>T		intron_variant	Intron 1 of 3	1		ENSP00000425184.1

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82828 AN: 151916 Hom.: 23721 Cov.: 32

Gnomad AFR AF: 0.719

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.354

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.494

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.545 AC: 82908 AN: 152032 Hom.: 23744 Cov.: 32 AF XY: 0.541 AC XY: 40176 AN XY: 74324

Gnomad4 AFR AF: 0.719 AC: 0.71941 AN: 0.71941

Gnomad4 AMR AF: 0.431 AC: 0.431202 AN: 0.431202

Gnomad4 ASJ AF: 0.509 AC: 0.508929 AN: 0.508929

Gnomad4 EAS AF: 0.354 AC: 0.353772 AN: 0.353772

Gnomad4 SAS AF: 0.491 AC: 0.491071 AN: 0.491071

Gnomad4 FIN AF: 0.499 AC: 0.499147 AN: 0.499147

Gnomad4 NFE AF: 0.494 AC: 0.493733 AN: 0.493733

Gnomad4 OTH AF: 0.532 AC: 0.532381 AN: 0.532381

Alfa AF: 0.501 Hom.: 31845

Bravo AF: 0.543

Asia WGS AF: 0.475 AC: 1653 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.42
DANN	Benign	0.75
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

Publications

LitVar

Other links and lift over

dbSNP: rs983889; hg19: chr5-15555486;