rs10489427

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_032785.4(AGBL4):​c.283-120993T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0486 in 152,260 control chromosomes in the GnomAD database, including 566 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 0.049 ( 566 hom., cov: 32)

Consequence

AGBL4
NM_032785.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.555
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 Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.157 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
AGBL4NM_032785.4 linkuse as main transcriptc.283-120993T>C intron_variant ENST00000371839.6 NP_116174.3 Q5VU57-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
AGBL4ENST00000371839.6 linkuse as main transcriptc.283-120993T>C intron_variant 2 NM_032785.4 ENSP00000360905.1 Q5VU57-1
AGBL4ENST00000371836.1 linkuse as main transcriptc.283-120993T>C intron_variant 1 ENSP00000360902.1 B1ANV5
AGBL4ENST00000371838.5 linkuse as main transcriptc.283-120993T>C intron_variant 5 ENSP00000360904.1 B1AMW3

Frequencies

GnomAD3 genomes
AF:
0.0485
AC:
7376
AN:
152142
Hom.:
565
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.160
Gnomad AMI
AF:
0.00110
Gnomad AMR
AF:
0.0289
Gnomad ASJ
AF:
0.00518
Gnomad EAS
AF:
0.000385
Gnomad SAS
AF:
0.000622
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.0380
Gnomad NFE
AF:
0.00263
Gnomad OTH
AF:
0.0441
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0486
AC:
7399
AN:
152260
Hom.:
566
Cov.:
32
AF XY:
0.0470
AC XY:
3496
AN XY:
74460
show subpopulations
Gnomad4 AFR
AF:
0.160
Gnomad4 AMR
AF:
0.0288
Gnomad4 ASJ
AF:
0.00518
Gnomad4 EAS
AF:
0.000386
Gnomad4 SAS
AF:
0.000622
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00262
Gnomad4 OTH
AF:
0.0436
Alfa
AF:
0.0118
Hom.:
106
Bravo
AF:
0.0552
Asia WGS
AF:
0.0110
AC:
39
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
5.4
DANN
Benign
0.77

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: rs10489427; hg19: chr1-49832529; API