rs114401766
Positions:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_000030.3(AGXT):c.166-56C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars).
Frequency
Genomes: 𝑓 0.00088 ( 0 hom., cov: 30)
Exomes 𝑓: 0.0054 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
AGXT
NM_000030.3 intron
NM_000030.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.266
Genes affected
AGXT (HGNC:341): (alanine--glyoxylate aminotransferase) This gene is expressed only in the liver and the encoded protein is localized mostly in the peroxisomes, where it is involved in glyoxylate detoxification. Mutations in this gene, some of which alter subcellular targetting, have been associated with type I primary hyperoxaluria. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGXT | NM_000030.3 | c.166-56C>T | intron_variant | ENST00000307503.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGXT | ENST00000307503.4 | c.166-56C>T | intron_variant | 1 | NM_000030.3 | P1 | |||
AGXT | ENST00000472436.1 | n.186-56C>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 94AN: 106498Hom.: 0 Cov.: 30 FAILED QC
GnomAD3 genomes
?
AF:
AC:
94
AN:
106498
Hom.:
Cov.:
30
FAILED QC
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00542 AC: 5704AN: 1052898Hom.: 0 Cov.: 31 AF XY: 0.00486 AC XY: 2569AN XY: 528282
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
5704
AN:
1052898
Hom.:
Cov.:
31
AF XY:
AC XY:
2569
AN XY:
528282
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.000882 AC: 94AN: 106582Hom.: 0 Cov.: 30 AF XY: 0.00107 AC XY: 56AN XY: 52436
GnomAD4 genome
?
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
94
AN:
106582
Hom.:
Cov.:
30
AF XY:
AC XY:
56
AN XY:
52436
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Primary hyperoxaluria, type I Uncertain:1
Uncertain significance, no assertion criteria provided | research | Clinical Biochemistry Laboratory, Health Services Laboratory | Nov 27, 2014 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at