5-35001212-A-T

Position:

• chr5-35001212-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_031900.4(AGXT2):​c.1438-2386T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 152,112 control chromosomes in the GnomAD database, including 19,218 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 0.50 (19218 hom., cov: 32)
• Consequence: AGXT2 NM_031900.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960

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]

AGXT2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.608 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AGXT2	NM_031900.4	c.1438-2386T>A		intron_variant		ENST00000231420.11	NP_114106.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AGXT2	ENST00000231420.11	c.1438-2386T>A		intron_variant		1	NM_031900.4	ENSP00000231420.6
AGXT2	ENST00000510428.1	c.1213-2386T>A		intron_variant		1		ENSP00000422799.1
AGXT2	ENST00000618015.4	c.1213-2386T>A		intron_variant		5		ENSP00000479154.1
AGXT2	ENST00000512135.5	n.1108-2386T>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.497 AC: 75594 AN: 151994 Hom.: 19199 Cov.: 32

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.444

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.497 AC: 75657 AN: 152112 Hom.: 19218 Cov.: 32 AF XY: 0.499 AC XY: 37134 AN XY: 74358

Gnomad4 AFR AF: 0.560

Gnomad4 AMR AF: 0.541

Gnomad4 ASJ AF: 0.473

Gnomad4 EAS AF: 0.626

Gnomad4 SAS AF: 0.559

Gnomad4 FIN AF: 0.447

Gnomad4 NFE AF: 0.444

Gnomad4 OTH AF: 0.489

Alfa AF: 0.479 Hom.: 2158

Bravo AF: 0.510

Asia WGS AF: 0.625 AC: 2171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.46
DANN	Benign	0.66

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

Publications

LitVar

Other links and lift over

dbSNP: rs163908; hg19: chr5-35001317;