5-35001212-A-T

Variant names:

• chr5-35001212-A-T
• rs163908
• NM_031900.4:c.1438-2386T>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.1438-2386T>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
• Publications: 6 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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.608 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.1438-2386T>A		intron	N/A	NP_114106.1	Q9BYV1-1
	AGXT2	NM_001438583.1		c.1435-2386T>A		intron	N/A	NP_001425512.1
	AGXT2	NM_001438584.1		c.1243-2386T>A		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.1438-2386T>A		intron	N/A	ENSP00000231420.6	Q9BYV1-1
	AGXT2	ENST00000510428.1	TSL:1	c.1213-2386T>A		intron	N/A	ENSP00000422799.1	Q9BYV1-2
	AGXT2	ENST00000853198.1		c.1519-2386T>A		intron	N/A	ENSP00000523257.1

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

African (AFR) AF: 0.560 AC: 23246 AN: 41494

American (AMR) AF: 0.541 AC: 8280 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1641 AN: 3472

East Asian (EAS) AF: 0.626 AC: 3232 AN: 5160

South Asian (SAS) AF: 0.559 AC: 2697 AN: 4826

European-Finnish (FIN) AF: 0.447 AC: 4731 AN: 10586

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.444 AC: 30207 AN: 67968

Other (OTH) AF: 0.489 AC: 1032 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.46
DANN	Benign	0.66
PhyloP100		-0.096
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: rs163908; hg19: chr5-35001317;