rs1343161

Positions:

• chr1-49645178-G-A
• chr1-49645178-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_032785.4(AGBL4):​c.282+52135C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.686 in 151,148 control chromosomes in the GnomAD database, including 36,302 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 0.69 (36302 hom., cov: 31)
• Consequence: AGBL4 NM_032785.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.254

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.777 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AGBL4	NM_032785.4	c.282+52135C>T		intron_variant		ENST00000371839.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AGBL4	ENST00000371839.6	c.282+52135C>T		intron_variant		2	NM_032785.4	P1
AGBL4	ENST00000371836.1	c.282+52135C>T		intron_variant		1
AGBL4	ENST00000371838.5	c.282+52135C>T		intron_variant		5
AGBL4	ENST00000497451.1	n.248+52135C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.686 AC: 103534 AN: 151028 Hom.: 36265 Cov.: 31

Gnomad AFR AF: 0.784

Gnomad AMI AF: 0.632

Gnomad AMR AF: 0.681

Gnomad ASJ AF: 0.759

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.717

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.697

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.686 AC: 103625 AN: 151148 Hom.: 36302 Cov.: 31 AF XY: 0.678 AC XY: 50077 AN XY: 73834

Gnomad4 AFR AF: 0.784

Gnomad4 AMR AF: 0.681

Gnomad4 ASJ AF: 0.759

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.675

Gnomad4 OTH AF: 0.696

Alfa AF: 0.689 Hom.: 6942

Bravo AF: 0.696

Asia WGS AF: 0.437 AC: 1512 AN: 3456

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.60
DANN	Benign	0.30

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

Other links and lift over

dbSNP: rs1343161; hg19: chr1-50110850;