chr1-48590923-C-T
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_032785.4(AGBL4):c.1014G>A(p.Met338Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000204 in 1,610,362 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.00014 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00021 ( 0 hom. )
Consequence
AGBL4
NM_032785.4 missense
NM_032785.4 missense
Scores
2
5
12
Clinical Significance
Conservation
PhyloP100: 7.46
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 Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.08206254).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGBL4 | NM_032785.4 | c.1014G>A | p.Met338Ile | missense_variant | 10/14 | ENST00000371839.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGBL4 | ENST00000371839.6 | c.1014G>A | p.Met338Ile | missense_variant | 10/14 | 2 | NM_032785.4 | P1 | |
AGBL4 | ENST00000416121.5 | c.552G>A | p.Met184Ile | missense_variant | 6/7 | 1 |
Frequencies
GnomAD3 genomes AF: 0.000145 AC: 22AN: 152114Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.000206 AC: 50AN: 243082Hom.: 0 AF XY: 0.000266 AC XY: 35AN XY: 131458
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GnomAD4 exome AF: 0.000210 AC: 306AN: 1458248Hom.: 0 Cov.: 31 AF XY: 0.000218 AC XY: 158AN XY: 724758
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GnomAD4 genome AF: 0.000145 AC: 22AN: 152114Hom.: 0 Cov.: 31 AF XY: 0.000148 AC XY: 11AN XY: 74302
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 26, 2023 | The c.1014G>A (p.M338I) alteration is located in exon 10 (coding exon 10) of the AGBL4 gene. This alteration results from a G to A substitution at nucleotide position 1014, causing the methionine (M) at amino acid position 338 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T;T
M_CAP
Benign
D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;.
REVEL
Uncertain
Sift
Benign
T;.
Sift4G
Benign
T;T
Polyphen
B;.
Vest4
MutPred
Gain of catalytic residue at M338 (P = 8e-04);.;
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
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