chr1-48590923-C-T

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

Scores

2
5
12

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 7.46
Variant links:
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]

Genome browser will be placed here

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
AGBL4NM_032785.4 linkuse as main transcriptc.1014G>A p.Met338Ile missense_variant 10/14 ENST00000371839.6

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
AGBL4ENST00000371839.6 linkuse as main transcriptc.1014G>A p.Met338Ile missense_variant 10/142 NM_032785.4 P1Q5VU57-1
AGBL4ENST00000416121.5 linkuse as main transcriptc.552G>A p.Met184Ile missense_variant 6/71

Frequencies

GnomAD3 genomes
AF:
0.000145
AC:
22
AN:
152114
Hom.:
0
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0000483
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000131
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000831
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000206
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000206
AC:
50
AN:
243082
Hom.:
0
AF XY:
0.000266
AC XY:
35
AN XY:
131458
show subpopulations
Gnomad AFR exome
AF:
0.000134
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000690
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000235
Gnomad OTH exome
AF:
0.000336
GnomAD4 exome
AF:
0.000210
AC:
306
AN:
1458248
Hom.:
0
Cov.:
31
AF XY:
0.000218
AC XY:
158
AN XY:
724758
show subpopulations
Gnomad4 AFR exome
AF:
0.0000598
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000252
Gnomad4 SAS exome
AF:
0.000660
Gnomad4 FIN exome
AF:
0.0000188
Gnomad4 NFE exome
AF:
0.000217
Gnomad4 OTH exome
AF:
0.0000829
GnomAD4 genome
AF:
0.000145
AC:
22
AN:
152114
Hom.:
0
Cov.:
31
AF XY:
0.000148
AC XY:
11
AN XY:
74302
show subpopulations
Gnomad4 AFR
AF:
0.0000483
Gnomad4 AMR
AF:
0.000131
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000831
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000206
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000238
Hom.:
0
Bravo
AF:
0.000140
TwinsUK
AF:
0.00
AC:
0
ALSPAC
AF:
0.000259
AC:
1
ESP6500AA
AF:
0.00
AC:
0
ESP6500EA
AF:
0.000242
AC:
2
ExAC
AF:
0.000248
AC:
30

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 submitterclinical testingAmbry GeneticsMay 26, 2023The 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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.88
BayesDel_addAF
Benign
-0.11
T
BayesDel_noAF
Uncertain
-0.030
CADD
Benign
22
DANN
Benign
0.96
DEOGEN2
Benign
0.0060
T;.
Eigen
Uncertain
0.23
Eigen_PC
Uncertain
0.41
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Benign
0.79
T;T
M_CAP
Benign
0.029
D
MetaRNN
Benign
0.082
T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.84
L;.
MutationTaster
Benign
1.0
D;D
PrimateAI
Uncertain
0.71
T
PROVEAN
Benign
-0.69
N;.
REVEL
Uncertain
0.32
Sift
Benign
0.65
T;.
Sift4G
Benign
0.95
T;T
Polyphen
0.016
B;.
Vest4
0.90
MutPred
0.61
Gain of catalytic residue at M338 (P = 8e-04);.;
MVP
0.12
MPC
0.38
ClinPred
0.056
T
GERP RS
5.8
Varity_R
0.20
gMVP
0.52

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs201706593; hg19: chr1-49056595; API