rs559668
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000278919.8(FEZ1):c.311+1587G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,114 control chromosomes in the GnomAD database, including 3,471 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 0.21 ( 3471 hom., cov: 32)
Consequence
FEZ1
ENST00000278919.8 intron
ENST00000278919.8 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.53
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]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FEZ1 | NM_005103.5 | c.311+1587G>A | intron_variant | ENST00000278919.8 | NP_005094.1 | |||
FEZ1 | XM_005271734.3 | c.311+1587G>A | intron_variant | XP_005271791.1 | ||||
FEZ1 | XM_005271735.3 | c.311+1587G>A | intron_variant | XP_005271792.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FEZ1 | ENST00000278919.8 | c.311+1587G>A | intron_variant | 1 | NM_005103.5 | ENSP00000278919 | P1 | |||
FEZ1 | ENST00000648911.1 | c.311+1587G>A | intron_variant | ENSP00000497070 | P1 | |||||
FEZ1 | ENST00000392709.8 | n.553+1587G>A | intron_variant, non_coding_transcript_variant | 2 | ||||||
FEZ1 | ENST00000532981.1 | n.454+1587G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.205 AC: 31163AN: 151996Hom.: 3459 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.205 AC: 31212AN: 152114Hom.: 3471 Cov.: 32 AF XY: 0.202 AC XY: 15058AN XY: 74364
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at