Variant rs466067 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_031900.4(AGXT2):c.1305T>C(p.Gly435Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.981 in 1,614,192 control chromosomes in the GnomAD database, including 778,423 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 0.95 ( 69204 hom., cov: 33)

Exomes 𝑓: 0.98 ( 709219 hom. )

Consequence

AGXT2
NM_031900.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.406

Variant links:

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 links:

AGXT2 (HGNC:):

AGXT2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.6).

BP7

Synonymous conserved (PhyloP=0.406 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.993 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AGXT2	NM_031900.4 linkuse as main transcript	c.1305T>C	p.Gly435Gly	synonymous_variant	12/14	ENST00000231420.11	NP_114106.1	Q9BYV1-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
AGXT2	ENST00000231420.11 linkuse as main transcript	c.1305T>C	p.Gly435Gly	synonymous_variant	12/14	1	NM_031900.4	ENSP00000231420.6	Q9BYV1-1
AGXT2	ENST00000510428.1 linkuse as main transcript	c.1080T>C	p.Gly360Gly	synonymous_variant	10/13	1		ENSP00000422799.1	Q9BYV1-2
AGXT2	ENST00000618015.4 linkuse as main transcript	c.1080T>C	p.Gly360Gly	synonymous_variant	10/12	5		ENSP00000479154.1	Q9BYV1-2
AGXT2	ENST00000512135.5 linkuse as main transcript	n.975T>C		non_coding_transcript_exon_variant	4/6	2

Frequencies

GnomAD3 genomes

AF:

0.951

AC:

144775

AN:

152186

Hom.:

69155

Cov.:

show subpopulations

Gnomad AFR

AF:

0.875

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.964

Gnomad ASJ

AF:

0.994

Gnomad EAS

AF:

0.800

Gnomad SAS

AF:

0.903

Gnomad FIN

AF:

1.00

Gnomad MID

AF:

0.987

Gnomad NFE

AF:

0.999

Gnomad OTH

AF:

0.959

GnomAD3 exomes

AF:

0.960

AC:

241374

AN:

251420

Hom.:

116369

AF XY:

0.961

AC XY:

130651

AN XY:

135888

show subpopulations

Gnomad AFR exome

AF:

0.870

Gnomad AMR exome

AF:

0.961

Gnomad ASJ exome

AF:

0.995

Gnomad EAS exome

AF:

0.804

Gnomad SAS exome

AF:

0.911

Gnomad FIN exome

AF:

0.999

Gnomad NFE exome

AF:

0.999

Gnomad OTH exome

AF:

0.981

GnomAD4 exome

AF:

0.984

AC:

1438664

AN:

1461888

Hom.:

709219

Cov.:

AF XY:

0.983

AC XY:

714539

AN XY:

727248

show subpopulations

Gnomad4 AFR exome

AF:

0.870

Gnomad4 AMR exome

AF:

0.960

Gnomad4 ASJ exome

AF:

0.995

Gnomad4 EAS exome

AF:

0.822

Gnomad4 SAS exome

AF:

0.911

Gnomad4 FIN exome

AF:

0.999

Gnomad4 NFE exome

AF:

1.00

Gnomad4 OTH exome

AF:

0.972

GnomAD4 genome

AF:

0.951

AC:

144878

AN:

152304

Hom.:

69204

Cov.:

AF XY:

0.950

AC XY:

70738

AN XY:

74480

show subpopulations

Gnomad4 AFR

AF:

0.875

Gnomad4 AMR

AF:

0.964

Gnomad4 ASJ

AF:

0.994

Gnomad4 EAS

AF:

0.800

Gnomad4 SAS

AF:

0.903

Gnomad4 FIN

AF:

1.00

Gnomad4 NFE

AF:

0.999

Gnomad4 OTH

AF:

0.960

Alfa

AF:

0.987

Hom.:

86711

Bravo

AF:

0.946

Asia WGS

AF:

0.857

AC:

2982

AN:

3478

EpiCase

AF:

0.999

EpiControl

AF:

0.999

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.60

CADD

Benign

6.6

DANN

Benign

0.74

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over