rs10893385

chr11-125479025-A-G

Variant summary

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

The NM_005103.5(FEZ1):c.411+2509T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 151,970 control chromosomes in the GnomAD database, including 18,215 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 0.47 (18215 hom., cov: 32)
• Consequence: FEZ1 NM_005103.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.25

Genes affected

FEZ1 (HGNC:3659): (fasciculation and elongation protein zeta 1) This gene is an ortholog of the C. elegans unc-76 gene, which is necessary for normal axonal bundling and elongation within axon bundles. Expression of this gene in C. elegans unc-76 mutants can restore to the mutants partial locomotion and axonal fasciculation, suggesting that it also functions in axonal outgrowth. The N-terminal half of the gene product is highly acidic. Alternatively spliced transcript variants encoding different isoforms of this protein have been described. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
FEZ1	NM_005103.5	c.411+2509T>C		intron_variant		ENST00000278919.8
FEZ1	XM_005271734.3	c.411+2509T>C		intron_variant
FEZ1	XM_005271735.3	c.411+2509T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
FEZ1	ENST00000278919.8	c.411+2509T>C		intron_variant		1	NM_005103.5	P1

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72066 AN: 151852 Hom.: 18219 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.613

Gnomad ASJ AF: 0.515

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.536

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.474 AC: 72075 AN: 151970 Hom.: 18215 Cov.: 32 AF XY: 0.476 AC XY: 35333 AN XY: 74270

Gnomad4 AFR AF: 0.293

Gnomad4 AMR AF: 0.612

Gnomad4 ASJ AF: 0.515

Gnomad4 EAS AF: 0.620

Gnomad4 SAS AF: 0.615

Gnomad4 FIN AF: 0.434

Gnomad4 NFE AF: 0.536

Gnomad4 OTH AF: 0.491

Alfa AF: 0.521 Hom.: 6782

Bravo AF: 0.479

Asia WGS AF: 0.560 AC: 1948 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.028
Dann	Benign	0.24

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: rs10893385; hg19: chr11-125348921;