rs180177178
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Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_000030.3(AGXT):c.166-47T>C 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 0.000066 ( 0 hom., cov: 29)
Exomes 𝑓: 0.000050 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
AGXT
NM_000030.3 intron
NM_000030.3 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -4.09
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AGXT | NM_000030.3 | c.166-47T>C | intron_variant | ENST00000307503.4 | NP_000021.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AGXT | ENST00000307503.4 | c.166-47T>C | intron_variant | 1 | NM_000030.3 | ENSP00000302620.3 | ||||
AGXT | ENST00000472436.1 | n.186-47T>C | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 7AN: 106034Hom.: 0 Cov.: 29 FAILED QC
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000499 AC: 53AN: 1062480Hom.: 0 Cov.: 31 AF XY: 0.0000412 AC XY: 22AN XY: 533436
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GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000660 AC: 7AN: 106034Hom.: 0 Cov.: 29 AF XY: 0.0000384 AC XY: 2AN XY: 52050
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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
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at