Variant chr2-240875890-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.777-45C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 1,598,714 control chromosomes in the GnomAD database, including 112,089 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.31 ( 8015 hom., cov: 34)

Exomes 𝑓: 0.37 ( 104074 hom. )

Consequence

AGXT
NM_000030.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts U:1B:2

Conservation

PhyloP100: -0.176

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:

AGXT (HGNC:):

AGXT links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 2-240875890-C-T is Benign according to our data. Variant chr2-240875890-C-T is described in ClinVar as [Benign]. Clinvar id is 204050.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AGXT	NM_000030.3 linkuse as main transcript	c.777-45C>T		intron_variant		ENST00000307503.4	NP_000021.1	P21549

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AGXT	ENST00000307503.4 linkuse as main transcript	c.777-45C>T		intron_variant		1	NM_000030.3	ENSP00000302620.3		P21549
AGXT	ENST00000476698.1 linkuse as main transcript	n.429-45C>T		intron_variant		5

Frequencies

GnomAD3 genomes

AF:

0.309

AC:

46936

AN:

151966

Hom.:

8014

Cov.:

show subpopulations

Gnomad AFR

AF:

0.168

Gnomad AMI

AF:

0.290

Gnomad AMR

AF:

0.269

Gnomad ASJ

AF:

0.340

Gnomad EAS

AF:

0.192

Gnomad SAS

AF:

0.230

Gnomad FIN

AF:

0.452

Gnomad MID

AF:

0.335

Gnomad NFE

AF:

0.394

Gnomad OTH

AF:

0.323

GnomAD3 exomes

AF:

0.325

AC:

80376

AN:

247112

Hom.:

14099

AF XY:

0.329

AC XY:

43961

AN XY:

133728

show subpopulations

Gnomad AFR exome

AF:

0.166

Gnomad AMR exome

AF:

0.240

Gnomad ASJ exome

AF:

0.345

Gnomad EAS exome

AF:

0.194

Gnomad SAS exome

AF:

0.236

Gnomad FIN exome

AF:

0.447

Gnomad NFE exome

AF:

0.394

Gnomad OTH exome

AF:

0.348

GnomAD4 exome

AF:

0.372

AC:

538410

AN:

1446630

Hom.:

104074

Cov.:

AF XY:

0.369

AC XY:

265947

AN XY:

720406

show subpopulations

Gnomad4 AFR exome

AF:

0.166

Gnomad4 AMR exome

AF:

0.242

Gnomad4 ASJ exome

AF:

0.339

Gnomad4 EAS exome

AF:

0.169

Gnomad4 SAS exome

AF:

0.241

Gnomad4 FIN exome

AF:

0.442

Gnomad4 NFE exome

AF:

0.400

Gnomad4 OTH exome

AF:

0.356

GnomAD4 genome

AF:

0.309

AC:

46945

AN:

152084

Hom.:

8015

Cov.:

AF XY:

0.308

AC XY:

22909

AN XY:

74324

show subpopulations

Gnomad4 AFR

AF:

0.168

Gnomad4 AMR

AF:

0.268

Gnomad4 ASJ

AF:

0.340

Gnomad4 EAS

AF:

0.191

Gnomad4 SAS

AF:

0.230

Gnomad4 FIN

AF:

0.452

Gnomad4 NFE

AF:

0.394

Gnomad4 OTH

AF:

0.322

Alfa

AF:

0.289

Hom.:

1227

Bravo

AF:

0.292

Asia WGS

AF:

0.210

AC:

730

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Uncertain:1Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	clinical testing	GeneDx	Aug 07, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

Primary hyperoxaluria, type I

Uncertain:1

Uncertain significance, no assertion criteria provided

research

Clinical Biochemistry Laboratory, Health Services Laboratory

Nov 27, 2014

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

2.7

DANN

Benign

0.82

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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