rs7930612

Variant names:

• chr11-47677846-C-A
• rs7930612
• NM_024783.4:c.2017-445G>T

Variant summary

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

The NM_024783.4(AGBL2):​c.2017-445G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 152,180 control chromosomes in the GnomAD database, including 1,203 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 0.12 (1203 hom., cov: 32)
• Consequence: AGBL2 NM_024783.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.146
• Publications: 7 publications found

Genes affected

AGBL2 (HGNC:26296): (AGBL carboxypeptidase 2) Predicted to enable metallocarboxypeptidase activity. Predicted to be involved in protein side chain deglutamylation. Located in centriole and ciliary basal body. [provided by Alliance of Genome Resources, Apr 2022]

AGBL2 Gene-Disease associations (from GenCC):

• epilepsy

  Inheritance: AR Classification: LIMITED Submitted by: Ambry Genetics

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.148 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024783.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AGBL2	NM_024783.4	MANE Select	c.2017-445G>T		intron	N/A	NP_079059.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AGBL2	ENST00000525123.6	TSL:1 MANE Select	c.2017-445G>T		intron	N/A	ENSP00000435582.1
	AGBL2	ENST00000528244.5	TSL:2	c.1903-445G>T		intron	N/A	ENSP00000436630.1
	AGBL2	ENST00000528609.5	TSL:1	n.*144-445G>T		intron	N/A	ENSP00000431912.1

Frequencies

GnomAD3 genomes AF: 0.119 AC: 18136 AN: 152062 Hom.: 1202 Cov.: 32

Gnomad AFR AF: 0.0871

Gnomad AMI AF: 0.0462

Gnomad AMR AF: 0.0989

Gnomad ASJ AF: 0.170

Gnomad EAS AF: 0.0411

Gnomad SAS AF: 0.0573

Gnomad FIN AF: 0.130

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.119 AC: 18138 AN: 152180 Hom.: 1203 Cov.: 32 AF XY: 0.116 AC XY: 8648 AN XY: 74400

African (AFR) AF: 0.0871 AC: 3616 AN: 41526

American (AMR) AF: 0.0987 AC: 1506 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.170 AC: 591 AN: 3472

East Asian (EAS) AF: 0.0410 AC: 213 AN: 5192

South Asian (SAS) AF: 0.0574 AC: 277 AN: 4826

European-Finnish (FIN) AF: 0.130 AC: 1374 AN: 10586

Middle Eastern (MID) AF: 0.123 AC: 36 AN: 292

European-Non Finnish (NFE) AF: 0.150 AC: 10229 AN: 68004

Other (OTH) AF: 0.120 AC: 254 AN: 2112

Alfa AF: 0.138 Hom.: 2722

Bravo AF: 0.117

Asia WGS AF: 0.0630 AC: 219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.5
DANN	Benign	0.50
PhyloP100		-0.15
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: rs7930612; hg19: chr11-47699398;