rs187490
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000231420.11(AGXT2):c.88+2783T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 152,068 control chromosomes in the GnomAD database, including 9,386 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 0.34 ( 9386 hom., cov: 32)
Consequence
AGXT2
ENST00000231420.11 intron
ENST00000231420.11 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.443
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 -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AGXT2 | NM_031900.4 | c.88+2783T>C | intron_variant | ENST00000231420.11 | NP_114106.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AGXT2 | ENST00000231420.11 | c.88+2783T>C | intron_variant | 1 | NM_031900.4 | ENSP00000231420 | P1 | |||
AGXT2 | ENST00000510428.1 | c.88+2783T>C | intron_variant | 1 | ENSP00000422799 | |||||
AGXT2 | ENST00000618015.4 | c.88+2783T>C | intron_variant | 5 | ENSP00000479154 | |||||
AGXT2 | ENST00000505542.1 | n.86+2783T>C | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.345 AC: 52365AN: 151948Hom.: 9376 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.345 AC: 52410AN: 152068Hom.: 9386 Cov.: 32 AF XY: 0.346 AC XY: 25737AN XY: 74320
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1315
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3478
ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
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