5-35000690-C-T

Variant names:

• chr5-35000690-C-T
• rs7717823
• NM_031900.4:c.1438-1864G>A

Variant summary

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

The NM_031900.4(AGXT2):​c.1438-1864G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.301 in 152,120 control chromosomes in the GnomAD database, including 7,773 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 0.30 (7773 hom., cov: 33)
• Consequence: AGXT2 NM_031900.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.471
• Publications: 13 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 (NFE) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AGXT2	NM_031900.4	c.1438-1864G>A		intron_variant	Intron 13 of 13	ENST00000231420.11	NP_114106.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
AGXT2	ENST00000231420.11	c.1438-1864G>A		intron_variant	Intron 13 of 13	1	NM_031900.4	ENSP00000231420.6
AGXT2	ENST00000510428.1	c.1213-1864G>A		intron_variant	Intron 11 of 12	1		ENSP00000422799.1
AGXT2	ENST00000618015.4	c.1213-1864G>A		intron_variant	Intron 11 of 11	5		ENSP00000479154.1
AGXT2	ENST00000512135.5	n.1108-1864G>A		intron_variant	Intron 5 of 5	2

Frequencies

GnomAD3 genomes AF: 0.301 AC: 45787 AN: 152002 Hom.: 7772 Cov.: 33

Gnomad AFR AF: 0.171

Gnomad AMI AF: 0.334

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.298

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.301 AC: 45793 AN: 152120 Hom.: 7773 Cov.: 33 AF XY: 0.300 AC XY: 22339 AN XY: 74382

African (AFR) AF: 0.171 AC: 7086 AN: 41510

American (AMR) AF: 0.280 AC: 4270 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1145 AN: 3472

East Asian (EAS) AF: 0.118 AC: 609 AN: 5172

South Asian (SAS) AF: 0.208 AC: 1003 AN: 4816

European-Finnish (FIN) AF: 0.420 AC: 4439 AN: 10572

Middle Eastern (MID) AF: 0.290 AC: 84 AN: 290

European-Non Finnish (NFE) AF: 0.386 AC: 26212 AN: 67992

Other (OTH) AF: 0.304 AC: 640 AN: 2108

Alfa AF: 0.347 Hom.: 27168

Bravo AF: 0.281

Asia WGS AF: 0.146 AC: 511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.8
DANN	Benign	0.63
PhyloP100		-0.47
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: rs7717823; hg19: chr5-35000795;