Variant 2-240874079-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000030.3(AGXT):c.680+17C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 1,610,752 control chromosomes in the GnomAD database, including 29,411 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.15 ( 2026 hom., cov: 33)

Exomes 𝑓: 0.19 ( 27385 hom. )

Consequence

AGXT
NM_000030.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts U:1B:4

Conservation

PhyloP100: -1.97

Variant links:

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]

AGXT links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.8).

BP6

Variant 2-240874079-C-T is Benign according to our data. Variant chr2-240874079-C-T is described in ClinVar as [Benign]. Clinvar id is 204043.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240874079-C-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AGXT	NM_000030.3 linkuse as main transcript	c.680+17C>T		intron_variant		ENST00000307503.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
AGXT	ENST00000307503.4 linkuse as main transcript	c.680+17C>T		intron_variant		1	NM_000030.3	P1
AGXT	ENST00000476698.1 linkuse as main transcript	n.332+1030C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.145

AC:

22121

AN:

152126

Hom.:

2023

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0604

Gnomad AMI

AF:

0.257

Gnomad AMR

AF:

0.120

Gnomad ASJ

AF:

0.179

Gnomad EAS

AF:

0.000965

Gnomad SAS

AF:

0.0732

Gnomad FIN

AF:

0.236

Gnomad MID

AF:

0.180

Gnomad NFE

AF:

0.201

Gnomad OTH

AF:

0.159

GnomAD3 exomes

AF:

0.148

AC:

36944

AN:

249928

Hom.:

3505

AF XY:

0.150

AC XY:

20278

AN XY:

135262

show subpopulations

Gnomad AFR exome

AF:

0.0613

Gnomad AMR exome

AF:

0.0809

Gnomad ASJ exome

AF:

0.182

Gnomad EAS exome

AF:

0.000327

Gnomad SAS exome

AF:

0.0723

Gnomad FIN exome

AF:

0.245

Gnomad NFE exome

AF:

0.203

Gnomad OTH exome

AF:

0.169

GnomAD4 exome

AF:

0.185

AC:

270108

AN:

1458508

Hom.:

27385

Cov.:

AF XY:

0.182

AC XY:

132203

AN XY:

725746

show subpopulations

Gnomad4 AFR exome

AF:

0.0609

Gnomad4 AMR exome

AF:

0.0838

Gnomad4 ASJ exome

AF:

0.178

Gnomad4 EAS exome

AF:

0.000328

Gnomad4 SAS exome

AF:

0.0763

Gnomad4 FIN exome

AF:

0.239

Gnomad4 NFE exome

AF:

0.207

Gnomad4 OTH exome

AF:

0.169

GnomAD4 genome

AF:

0.145

AC:

22126

AN:

152244

Hom.:

2026

Cov.:

AF XY:

0.144

AC XY:

10700

AN XY:

74440

show subpopulations

Gnomad4 AFR

AF:

0.0604

Gnomad4 AMR

AF:

0.119

Gnomad4 ASJ

AF:

0.179

Gnomad4 EAS

AF:

0.000967

Gnomad4 SAS

AF:

0.0741

Gnomad4 FIN

AF:

0.236

Gnomad4 NFE

AF:

0.201

Gnomad4 OTH

AF:

0.157

Alfa

AF:

0.128

Hom.:

315

Bravo

AF:

0.135

Asia WGS

AF:

0.0340

AC:

117

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Uncertain:1Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Primary hyperoxaluria, type I

Uncertain:1Benign:1

Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 10, 2021	- -
Uncertain significance, no assertion criteria provided	research	Clinical Biochemistry Laboratory, Health Services Laboratory	Nov 27, 2014	- -

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

2.1

DANN

Benign

0.88

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over