rs10520642

chr15-86856866-T-C

Variant summary

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

The NM_001386094.1(AGBL1):c.3159-50221T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0183 in 152,340 control chromosomes in the GnomAD database, including 49 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 0.018 (49 hom., cov: 33)
• Consequence: AGBL1 NM_001386094.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.695

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=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AGBL1	NM_001386094.1	c.3159-50221T>C		intron_variant		ENST00000614907.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AGBL1	ENST00000614907.3	c.3159-50221T>C		intron_variant		5	NM_001386094.1	P4
AGBL1	ENST00000441037.7	c.3222-131121T>C		intron_variant		5		A2
AGBL1	ENST00000681381.1	n.317+182430T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0182 AC: 2776 AN: 152222 Hom.: 47 Cov.: 33

Gnomad AFR AF: 0.0228

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0157

Gnomad ASJ AF: 0.0225

Gnomad EAS AF: 0.0133

Gnomad SAS AF: 0.0671

Gnomad FIN AF: 0.00640

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0145

Gnomad OTH AF: 0.0196

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

GnomAD4 genome AF: 0.0183 AC: 2793 AN: 152340 Hom.: 49 Cov.: 33 AF XY: 0.0192 AC XY: 1432 AN XY: 74500

Gnomad4 AFR AF: 0.0231

Gnomad4 AMR AF: 0.0157

Gnomad4 ASJ AF: 0.0225

Gnomad4 EAS AF: 0.0135

Gnomad4 SAS AF: 0.0671

Gnomad4 FIN AF: 0.00640

Gnomad4 NFE AF: 0.0145

Gnomad4 OTH AF: 0.0194

Alfa AF: 0.0159 Hom.: 5

Bravo AF: 0.0176

Asia WGS AF: 0.0500 AC: 174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	0.088
Dann	Benign	0.69

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: rs10520642; hg19: chr15-87400097;