rs466067
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1
The NM_031900.4(AGXT2):āc.1305T>Cā(p.Gly435=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.981 in 1,614,192 control chromosomes in the GnomAD database, including 778,423 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: š 0.95 ( 69204 hom., cov: 33)
Exomes š: 0.98 ( 709219 hom. )
Consequence
AGXT2
NM_031900.4 synonymous
NM_031900.4 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.406
Genes affected
AGXT2 (HGNC:14412): (alanine--glyoxylate aminotransferase 2) The protein encoded by this gene is a class III pyridoxal-phosphate-dependent mitochondrial aminotransferase. It catalyzes the conversion of glyoxylate to glycine using L-alanine as the amino donor. It is an important regulator of methylarginines and is involved in the control of blood pressure in kidney. Polymorphisms in this gene affect methylarginine and beta-aminoisobutyrate metabolism, and are associated with carotid atherosclerosis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP7
?
Synonymous conserved (PhyloP=0.406 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGXT2 | NM_031900.4 | c.1305T>C | p.Gly435= | synonymous_variant | 12/14 | ENST00000231420.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGXT2 | ENST00000231420.11 | c.1305T>C | p.Gly435= | synonymous_variant | 12/14 | 1 | NM_031900.4 | P1 | |
AGXT2 | ENST00000510428.1 | c.1080T>C | p.Gly360= | synonymous_variant | 10/13 | 1 | |||
AGXT2 | ENST00000618015.4 | c.1080T>C | p.Gly360= | synonymous_variant | 10/12 | 5 | |||
AGXT2 | ENST00000512135.5 | n.975T>C | non_coding_transcript_exon_variant | 4/6 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.951 AC: 144775AN: 152186Hom.: 69155 Cov.: 33
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GnomAD3 exomes AF: 0.960 AC: 241374AN: 251420Hom.: 116369 AF XY: 0.961 AC XY: 130651AN XY: 135888
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GnomAD4 exome AF: 0.984 AC: 1438664AN: 1461888Hom.: 709219 Cov.: 65 AF XY: 0.983 AC XY: 714539AN XY: 727248
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GnomAD4 genome ? AF: 0.951 AC: 144878AN: 152304Hom.: 69204 Cov.: 33 AF XY: 0.950 AC XY: 70738AN XY: 74480
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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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