rs4675792

Positions:

• chr2-240880109-C-T

Variant summary

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

The NM_000030.3(AGXT):​c.*1288C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 152,018 control chromosomes in the GnomAD database, including 21,548 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 0.52 (21545 hom., cov: 32)
  • Exomes 𝑓: 1.0 (3 hom.)
• Consequence: AGXT NM_000030.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.195

Genes affected

AGXT (HGNC:341): (alanine--glyoxylate aminotransferase) This gene is expressed only in the liver and the encoded protein is localized mostly in the peroxisomes, where it is involved in glyoxylate detoxification. Mutations in this gene, some of which alter subcellular targetting, have been associated with type I primary hyperoxaluria. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AGXT	NM_000030.3	c.*1288C>T		3_prime_UTR_variant	11/11	ENST00000307503.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AGXT	ENST00000307503.4	c.*1288C>T		3_prime_UTR_variant	11/11	1	NM_000030.3	P1
AGXT	ENST00000470255.1	n.2245C>T		non_coding_transcript_exon_variant	3/3	2

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78872 AN: 151894 Hom.: 21538 Cov.: 32

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.487

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.678

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.605

Gnomad OTH AF: 0.528

GnomAD4 exome AF: 1.00 AC: 6 AN: 6 Hom.: 3 Cov.: 0 AF XY: 1.00 AC XY: 4 AN XY: 4

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 1.00

GnomAD4 genome AF: 0.519 AC: 78905 AN: 152012 Hom.: 21545 Cov.: 32 AF XY: 0.518 AC XY: 38517 AN XY: 74322

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.487

Gnomad4 ASJ AF: 0.481

Gnomad4 EAS AF: 0.586

Gnomad4 SAS AF: 0.394

Gnomad4 FIN AF: 0.678

Gnomad4 NFE AF: 0.605

Gnomad4 OTH AF: 0.524

Alfa AF: 0.577 Hom.: 32990

Bravo AF: 0.501

Asia WGS AF: 0.472 AC: 1645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.7
DANN	Benign	0.48

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4675792; hg19: chr2-241819526;