1-49824429-C-T

Variant summary

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

The NM_032785.4(AGBL4):​c.157+26967G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 152,030 control chromosomes in the GnomAD database, including 16,091 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 0.42 ( 16091 hom., cov: 32)

Consequence

AGBL4
NM_032785.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00400
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]

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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 = 0.562 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
AGBL4NM_032785.4 linkuse as main transcriptc.157+26967G>A intron_variant ENST00000371839.6 NP_116174.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
AGBL4ENST00000371839.6 linkuse as main transcriptc.157+26967G>A intron_variant 2 NM_032785.4 ENSP00000360905 P1Q5VU57-1
AGBL4ENST00000371836.1 linkuse as main transcriptc.157+26967G>A intron_variant 1 ENSP00000360902
AGBL4ENST00000371838.5 linkuse as main transcriptc.157+26967G>A intron_variant 5 ENSP00000360904
AGBL4ENST00000497451.1 linkuse as main transcriptn.123+26967G>A intron_variant, non_coding_transcript_variant 2

Frequencies

GnomAD3 genomes
AF:
0.423
AC:
64295
AN:
151912
Hom.:
16091
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.183
Gnomad AMI
AF:
0.516
Gnomad AMR
AF:
0.477
Gnomad ASJ
AF:
0.591
Gnomad EAS
AF:
0.0392
Gnomad SAS
AF:
0.415
Gnomad FIN
AF:
0.483
Gnomad MID
AF:
0.535
Gnomad NFE
AF:
0.566
Gnomad OTH
AF:
0.468
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.423
AC:
64299
AN:
152030
Hom.:
16091
Cov.:
32
AF XY:
0.417
AC XY:
31017
AN XY:
74304
show subpopulations
Gnomad4 AFR
AF:
0.182
Gnomad4 AMR
AF:
0.476
Gnomad4 ASJ
AF:
0.591
Gnomad4 EAS
AF:
0.0397
Gnomad4 SAS
AF:
0.416
Gnomad4 FIN
AF:
0.483
Gnomad4 NFE
AF:
0.566
Gnomad4 OTH
AF:
0.463
Alfa
AF:
0.495
Hom.:
9699
Bravo
AF:
0.411
Asia WGS
AF:
0.206
AC:
718
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.60
DANN
Benign
0.57

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: rs4926831; hg19: chr1-50290101; API