15-86484083-A-G

Position:

• chr15-86484083-A-G

Variant summary

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

The NM_001386094.1(AGBL1):​c.2556-38727A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0773 in 152,190 control chromosomes in the GnomAD database, including 1,128 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 0.077 (1128 hom., cov: 33)
• Consequence: AGBL1 NM_001386094.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.382

Genes affected

AGBL1 (HGNC:26504): (AGBL carboxypeptidase 1) Polyglutamylation is a reversible posttranslational modification catalyzed by polyglutamylases that results in the addition of glutamate side chains on the modified protein. This gene encodes a glutamate decarboxylase that catalyzes the deglutamylation of polyglutamylated proteins. Mutations in this gene result in dominant late-onset Fuchs corneal dystrophy. [provided by RefSeq, Nov 2013]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AGBL1	NM_001386094.1	c.2556-38727A>G		intron_variant		ENST00000614907.3	NP_001373023.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AGBL1	ENST00000614907.3	c.2556-38727A>G		intron_variant		5	NM_001386094.1	ENSP00000490608.2
AGBL1	ENST00000441037.7	c.2556-38727A>G		intron_variant		5		ENSP00000413001.3

Frequencies

GnomAD3 genomes AF: 0.0772 AC: 11741 AN: 152072 Hom.: 1125 Cov.: 33

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0351

Gnomad ASJ AF: 0.0294

Gnomad EAS AF: 0.00638

Gnomad SAS AF: 0.00993

Gnomad FIN AF: 0.0143

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0192

Gnomad OTH AF: 0.0594

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

GnomAD4 genome AF: 0.0773 AC: 11763 AN: 152190 Hom.: 1128 Cov.: 33 AF XY: 0.0749 AC XY: 5571 AN XY: 74424

Gnomad4 AFR AF: 0.228

Gnomad4 AMR AF: 0.0350

Gnomad4 ASJ AF: 0.0294

Gnomad4 EAS AF: 0.00639

Gnomad4 SAS AF: 0.00973

Gnomad4 FIN AF: 0.0143

Gnomad4 NFE AF: 0.0192

Gnomad4 OTH AF: 0.0588

Alfa AF: 0.0256 Hom.: 257

Bravo AF: 0.0851

Asia WGS AF: 0.0200 AC: 70 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	2.6
DANN	Benign	0.81

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: rs7175159; hg19: chr15-87027314;