rs4732082

Variant names:

• chr7-135033654-G-A
• rs4732082
• NM_178563.4:c.558-495G>A

Your query was ambiguous. Multiple possible variants found:

• chr7-135033654-G-A
• chr7-135033654-G-C
• chr7-135033654-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_178563.4(AGBL3):​c.558-495G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.443 in 152,080 control chromosomes in the GnomAD database, including 15,583 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 0.44 (15583 hom., cov: 32)
• Consequence: AGBL3 NM_178563.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.59
• Publications: 7 publications found

Genes affected

AGBL3 (HGNC:27981): (AGBL carboxypeptidase 3) Enables metallocarboxypeptidase activity. Involved in protein side chain deglutamylation. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000286458 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.757 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_178563.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AGBL3	NM_178563.4	MANE Select	c.558-495G>A		intron	N/A	NP_848658.3	Q8NEM8-4
	AGBL3	NM_001345850.1		c.4-10371G>A		intron	N/A	NP_001332779.1
	AGBL3	NM_001345851.1		c.4-10371G>A		intron	N/A	NP_001332780.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AGBL3	ENST00000436302.6	TSL:2 MANE Select	c.558-495G>A		intron	N/A	ENSP00000388275.2	Q8NEM8-4
	AGBL3	ENST00000275763.10	TSL:1	n.558-495G>A		intron	N/A	ENSP00000275763.6	Q8NEM8-2
	AGBL3	ENST00000435976.6	TSL:5	c.558-495G>A		intron	N/A	ENSP00000401220.2	F8W7R4

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67406 AN: 151962 Hom.: 15584 Cov.: 32

Gnomad AFR AF: 0.337

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.463

Gnomad ASJ AF: 0.343

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.520

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.457

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

GnomAD4 genome AF: 0.443 AC: 67430 AN: 152080 Hom.: 15583 Cov.: 32 AF XY: 0.445 AC XY: 33096 AN XY: 74340

African (AFR) AF: 0.337 AC: 13987 AN: 41496

American (AMR) AF: 0.463 AC: 7075 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.343 AC: 1192 AN: 3472

East Asian (EAS) AF: 0.777 AC: 4022 AN: 5178

South Asian (SAS) AF: 0.333 AC: 1607 AN: 4826

European-Finnish (FIN) AF: 0.520 AC: 5487 AN: 10546

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.481 AC: 32663 AN: 67962

Other (OTH) AF: 0.456 AC: 964 AN: 2112

Alfa AF: 0.460 Hom.: 2927

Bravo AF: 0.440

Asia WGS AF: 0.495 AC: 1717 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	16
DANN	Benign	0.62
PhyloP100		1.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4732082; hg19: chr7-134718405; COSMIC: COSV51952772;