11-47677846-C-A

Position:

• chr11-47677846-C-A

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AGBL2	NM_024783.4	c.2017-445G>T		intron_variant		ENST00000525123.6	NP_079059.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AGBL2	ENST00000525123.6	c.2017-445G>T		intron_variant		1	NM_024783.4	ENSP00000435582	P2
AGBL2	ENST00000528609.5	c.*144-445G>T		intron_variant, NMD_transcript_variant		1		ENSP00000431912
AGBL2	ENST00000528244.5	c.1903-445G>T		intron_variant		2		ENSP00000436630	A2
AGBL2	ENST00000529712.5	n.2550+2127G>T		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.0871

Gnomad4 AMR AF: 0.0987

Gnomad4 ASJ AF: 0.170

Gnomad4 EAS AF: 0.0410

Gnomad4 SAS AF: 0.0574

Gnomad4 FIN AF: 0.130

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.120

Alfa AF: 0.142 Hom.: 2010

Bravo AF: 0.117

Asia WGS AF: 0.0630 AC: 219 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	1.5
DANN	Benign	0.50

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: rs7930612; hg19: chr11-47699398;