rs574329
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_032785.4(AGBL4):c.378-86946G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.482 in 151,986 control chromosomes in the GnomAD database, including 20,460 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 0.48 ( 20460 hom., cov: 32)
Consequence
AGBL4
NM_032785.4 intron
NM_032785.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.305
Genes affected
AGBL4 (HGNC:25892): (AGBL carboxypeptidase 4) Predicted to enable metallocarboxypeptidase activity and tubulin binding activity. Predicted to be involved in C-terminal protein deglutamylation; defense response to virus; and protein side chain deglutamylation. Predicted to act upstream of or within several processes, including axonal transport of mitochondrion; positive regulation of ubiquitin-dependent protein catabolic process; and regulation of blastocyst development. Located in Golgi apparatus; centriole; and ciliary basal body. [provided by Alliance of Genome Resources, Apr 2022]
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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 (NFE) allele frequency at 95% confidence interval = 0.628 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGBL4 | NM_032785.4 | c.378-86946G>A | intron_variant | ENST00000371839.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGBL4 | ENST00000371839.6 | c.378-86946G>A | intron_variant | 2 | NM_032785.4 | P1 | |||
AGBL4 | ENST00000371836.1 | c.378-86946G>A | intron_variant | 1 | |||||
ENST00000456002.2 | n.179-42066C>T | intron_variant, non_coding_transcript_variant | 5 | ||||||
AGBL4 | ENST00000371838.5 | c.378-86946G>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.483 AC: 73308AN: 151868Hom.: 20457 Cov.: 32
GnomAD3 genomes
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.482 AC: 73329AN: 151986Hom.: 20460 Cov.: 32 AF XY: 0.476 AC XY: 35376AN XY: 74274
GnomAD4 genome
?
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73329
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151986
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32
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35376
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74274
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1054
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
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