chr15-86935142-G-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000560696.1(ENSG00000259636):​n.150G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)

Consequence

ENSG00000259636
ENST00000560696.1 non_coding_transcript_exon

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.716

Publications

3 publications found
Variant links:
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]
AGBL1 Gene-Disease associations (from GenCC):
  • Fuchs' endothelial dystrophy
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • corneal dystrophy, Fuchs endothelial, 8
    Inheritance: AD Classification: LIMITED Submitted by: G2P

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC105370954NR_135682.1 linkn.150G>T non_coding_transcript_exon_variant Exon 2 of 3
AGBL1NM_152336.4 linkc.3222-52845G>T intron_variant Intron 23 of 24 NP_689549.3 Q96MI9
AGBL1XM_011521227.4 linkc.3159-93683G>T intron_variant Intron 22 of 22 XP_011519529.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000259636ENST00000560696.1 linkn.150G>T non_coding_transcript_exon_variant Exon 2 of 3 3
AGBL1ENST00000441037.7 linkc.3222-52845G>T intron_variant Intron 23 of 24 5 ENSP00000413001.3 Q96MI9
AGBL1ENST00000681381.1 linkn.318-106863G>T intron_variant Intron 2 of 3

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
0
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.00
Hom.:
353

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.89
CADD
Benign
2.8
DANN
Benign
0.54
PhyloP100
0.72

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

Other links and lift over

dbSNP: rs1433456; hg19: chr15-87478373; API