chr22-32475396-T-C

Position:

• chr22-32475396-T-C

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001033024.2(FBXO7):​c.35T>C​(p.Leu12Pro) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/17 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L12R) has been classified as Benign.

• Frequency: Genomes: not found (cov: 33)
• Consequence: FBXO7 NM_001033024.2 missense, splice_region
• Scores: Splicing: ADA: 0.00005583
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.301

Genes affected

FBXO7 (HGNC:13586): (F-box protein 7) 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 the 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 Fbxs class and it may play a role in regulation of hematopoiesis. Alternatively spliced transcript variants of this gene have been identified with the full-length natures of only some variants being determined. [provided by RefSeq, Jul 2008]

FBXO7 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.037294954).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
FBXO7	NM_012179.4	c.122+272T>C		intron_variant		ENST00000266087.12	NP_036311.3
FBXO7	NM_001033024.2	c.35T>C	p.Leu12Pro	missense_variant, splice_region_variant	1/9		NP_001028196.1
FBXO7	NM_001257990.2	c.-223T>C		splice_region_variant	1/9		NP_001244919.1
FBXO7	NM_001257990.2	c.-223T>C		5_prime_UTR_variant	1/9		NP_001244919.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FBXO7	ENST00000266087.12	c.122+272T>C		intron_variant		1	NM_012179.4	ENSP00000266087.7

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 36

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.26	T
BayesDel_noAF	Benign	-0.62
CADD	Benign	5.4
DANN	Benign	0.54
Eigen	Benign	-1.6
Eigen_PC	Benign	-1.7
FATHMM_MKL	Benign	0.0087	N
LIST_S2	Benign	0.31	T
M_CAP	Benign	0.0033	T
MetaRNN	Benign	0.037	T
MetaSVM	Benign	-1.1	T
PROVEAN	Benign	0.79	N
REVEL	Benign	0.14
Sift	Benign	0.22	T
Sift4G	Benign	0.38	T
Polyphen		0.0	B
Vest4		0.040
MutPred		0.074		Loss of stability (P = 0.0383);
MVP		0.030
ClinPred		0.091	T
GERP RS		-6.1

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Benign	0.000056
dbscSNV1_RF	Benign	0.0
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: rs8137714; hg19: chr22-32871383;