5-35044193-C-G

Variant names:

• chr5-35044193-C-G
• rs28305
• NM_031900.4:c.89-3530G>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.89-3530G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.891 in 152,226 control chromosomes in the GnomAD database, including 61,182 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 0.89 (61182 hom., cov: 31)
• Consequence: AGXT2 NM_031900.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.329
• Publications: 12 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.965 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AGXT2	NM_031900.4	MANE Select	c.89-3530G>C		intron	N/A	NP_114106.1	Q9BYV1-1
	AGXT2	NM_001438583.1		c.89-3533G>C		intron	N/A	NP_001425512.1
	AGXT2	NM_001438584.1		c.89-3530G>C		intron	N/A	NP_001425513.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AGXT2	ENST00000231420.11	TSL:1 MANE Select	c.89-3530G>C		intron	N/A	ENSP00000231420.6	Q9BYV1-1
	AGXT2	ENST00000510428.1	TSL:1	c.89-3530G>C		intron	N/A	ENSP00000422799.1	Q9BYV1-2
	AGXT2	ENST00000853198.1		c.169+199G>C		intron	N/A	ENSP00000523257.1

Frequencies

GnomAD3 genomes AF: 0.891 AC: 135595 AN: 152108 Hom.: 61124 Cov.: 31

Gnomad AFR AF: 0.973

Gnomad AMI AF: 0.919

Gnomad AMR AF: 0.775

Gnomad ASJ AF: 0.879

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.831

Gnomad FIN AF: 0.900

Gnomad MID AF: 0.918

Gnomad NFE AF: 0.897

Gnomad OTH AF: 0.898

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

GnomAD4 genome AF: 0.891 AC: 135705 AN: 152226 Hom.: 61182 Cov.: 31 AF XY: 0.887 AC XY: 66025 AN XY: 74424

African (AFR) AF: 0.973 AC: 40431 AN: 41570

American (AMR) AF: 0.774 AC: 11837 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.879 AC: 3048 AN: 3466

East Asian (EAS) AF: 0.547 AC: 2811 AN: 5138

South Asian (SAS) AF: 0.832 AC: 4015 AN: 4826

European-Finnish (FIN) AF: 0.900 AC: 9542 AN: 10600

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.897 AC: 61022 AN: 68018

Other (OTH) AF: 0.895 AC: 1891 AN: 2114

Alfa AF: 0.865 Hom.: 2781

Bravo AF: 0.880

Asia WGS AF: 0.724 AC: 2516 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.96
DANN	Benign	0.51
PhyloP100		-0.33
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: rs28305; hg19: chr5-35044298;