NM_031900.4:c.487-158T>C

Variant names:

• chr5-35035474-A-G
• rs344156
• NM_031900.4:c.487-158T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_031900.4(AGXT2):​c.487-158T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.664 in 152,072 control chromosomes in the GnomAD database, including 33,595 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 0.66 (33595 hom., cov: 32)
• Consequence: AGXT2 NM_031900.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.199
• Publications: 7 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.752 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_031900.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AGXT2	NM_031900.4	MANE Select	c.487-158T>C		intron	N/A	NP_114106.1
	AGXT2	NM_001438583.1		c.484-158T>C		intron	N/A	NP_001425512.1
	AGXT2	NM_001438584.1		c.487-158T>C		intron	N/A	NP_001425513.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AGXT2	ENST00000231420.11	TSL:1 MANE Select	c.487-158T>C		intron	N/A	ENSP00000231420.6
	AGXT2	ENST00000510428.1	TSL:1	c.487-158T>C		intron	N/A	ENSP00000422799.1
	AGXT2	ENST00000853198.1		c.568-158T>C		intron	N/A	ENSP00000523257.1

Frequencies

GnomAD3 genomes AF: 0.664 AC: 100851 AN: 151954 Hom.: 33581 Cov.: 32

Gnomad AFR AF: 0.643

Gnomad AMI AF: 0.805

Gnomad AMR AF: 0.715

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.773

Gnomad FIN AF: 0.626

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.659

Gnomad OTH AF: 0.672

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.664 AC: 100905 AN: 152072 Hom.: 33595 Cov.: 32 AF XY: 0.664 AC XY: 49345 AN XY: 74310

African (AFR) AF: 0.642 AC: 26626 AN: 41466

American (AMR) AF: 0.715 AC: 10936 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2379 AN: 3468

East Asian (EAS) AF: 0.669 AC: 3454 AN: 5166

South Asian (SAS) AF: 0.773 AC: 3719 AN: 4814

European-Finnish (FIN) AF: 0.626 AC: 6605 AN: 10550

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.659 AC: 44827 AN: 67998

Other (OTH) AF: 0.673 AC: 1421 AN: 2112

Alfa AF: 0.669 Hom.: 57189

Bravo AF: 0.673

Asia WGS AF: 0.704 AC: 2446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.56
DANN	Benign	0.43
PhyloP100		-0.20
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs344156; hg19: chr5-35035579;