rs117195882

Variant names:

Variant summary

Our verdict is Benign. The variant received -17 ACMG points: 3P and 20B. PM1PP2BP4_StrongBP6_Very_StrongBA1

The NM_000030.3(AGXT):c.557C>T(p.Ala186Val) variant causes a missense change. The variant allele was found at a frequency of 0.00453 in 1,613,864 control chromosomes in the GnomAD database, including 207 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).

Frequency

Genomes: 𝑓 0.0041 ( 22 hom., cov: 32)

Exomes 𝑓: 0.0046 ( 185 hom. )

Consequence

AGXT
NM_000030.3 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: 4.09

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 was made for transcript

Our verdict: Benign. The variant received -17 ACMG points.

PM1

In a hotspot region, there are 6 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 4 uncertain in NM_000030.3

PP2

Missense variant in the gene, where a lot of missense mutations are associated with disease in ClinVar. The gene has 130 curated pathogenic missense variants (we use a threshold of 10). The gene has 12 curated benign missense variants. Gene score misZ: -0.26789 (below the threshold of 3.09). Trascript score misZ: -0.48778 (below the threshold of 3.09). GenCC associations: The gene is linked to primary hyperoxaluria type 1, alanine glyoxylate aminotransferase deficiency.

BP4

Computational evidence support a benign effect (MetaRNN=0.01129064).

BP6

Variant 2-240873011-C-T is Benign according to our data. Variant chr2-240873011-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 92311.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-240873011-C-T is described in Lovd as [Likely_pathogenic].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
AGXT	NM_000030.3 link	c.557C>T	p.Ala186Val	missense_variant	Exon 5 of 11	ENST00000307503.4	NP_000021.1	P21549

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
AGXT	ENST00000307503.4 link	c.557C>T	p.Ala186Val	missense_variant	Exon 5 of 11	1	NM_000030.3	ENSP00000302620.3	P21549
AGXT	ENST00000472436.1 link	n.577C>T		non_coding_transcript_exon_variant	Exon 5 of 5	2
AGXT	ENST00000476698.1 link	n.294C>T		non_coding_transcript_exon_variant	Exon 2 of 4	5

Frequencies

GnomAD3 genomes

AF:

0.00410

AC:

624

AN:

152162

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000338

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00190

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.0719

Gnomad SAS

AF:

0.0298

Gnomad FIN

AF:

0.00122

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000588

Gnomad OTH

AF:

0.00574

GnomAD2 exomes

AF:

0.0113

AC:

2811

AN:

249728

AF XY:

0.0119

show subpopulations

Gnomad AFR exome

AF:

0.000246

Gnomad AMR exome

AF:

0.00521

Gnomad ASJ exome

AF:

0.000199

Gnomad EAS exome

AF:

0.0868

Gnomad FIN exome

AF:

0.000370

Gnomad NFE exome

AF:

0.000883

Gnomad OTH exome

AF:

0.00473

GnomAD4 exome

AF:

0.00457

AC:

6684

AN:

1461584

Hom.:

185

Cov.:

AF XY:

0.00527

AC XY:

3835

AN XY:

727114

show subpopulations

Gnomad4 AFR exome

AF:

0.000209

AC:

AN:

33480

Gnomad4 AMR exome

AF:

0.00483

AC:

216

AN:

44712

Gnomad4 ASJ exome

AF:

0.0000383

AC:

AN:

26126

Gnomad4 EAS exome

AF:

0.0768

AC:

3046

AN:

39678

Gnomad4 SAS exome

AF:

0.0281

AC:

2423

AN:

86204

Gnomad4 FIN exome

AF:

0.000694

AC:

AN:

53338

Gnomad4 NFE exome

AF:

0.000564

AC:

627

AN:

1111902

Gnomad4 Remaining exome

AF:

0.00525

AC:

317

AN:

60378

Heterozygous variant carriers

351

702

1053

1404

1755

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Exome Het

Exome Hom

Variant carriers

196

294

392

490

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00408

AC:

622

AN:

152280

Hom.:

Cov.:

AF XY:

0.00496

AC XY:

369

AN XY:

74440

show subpopulations

Gnomad4 AFR

AF:

0.000337

AC:

0.000336765

AN:

0.000336765

Gnomad4 AMR

AF:

0.00189

AC:

0.00189468

AN:

0.00189468

Gnomad4 ASJ

AF:

0.00

AC:

AN:

Gnomad4 EAS

AF:

0.0719

AC:

0.0718992

AN:

0.0718992

Gnomad4 SAS

AF:

0.0296

AC:

0.0296312

AN:

0.0296312

Gnomad4 FIN

AF:

0.00122

AC:

0.00122387

AN:

0.00122387

Gnomad4 NFE

AF:

0.000588

AC:

0.000588183

AN:

0.000588183

Gnomad4 OTH

AF:

0.00568

AC:

0.00567644

AN:

0.00567644

Heterozygous variant carriers

102

136

170

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Genome Het

Genome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00306

Hom.:

Bravo

AF:

0.00413

TwinsUK

AF:

0.000809

AC:

ALSPAC

AF:

0.00182

AC:

ESP6500AA

AF:

0.000681

AC:

ESP6500EA

AF:

0.000698

AC:

ExAC

AF:

0.0114

AC:

1384

Asia WGS

AF:

0.0370

AC:

129

AN:

3478

EpiCase

AF:

0.000600

EpiControl

AF:

0.000711

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:8

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Primary hyperoxaluria, type I

Benign:4

Oct 27, 2023

Clinical Biochemistry Laboratory, Health Services Laboratory

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Found in cis with c.590G>A in 2 unrelated individuals. ACMG:PM2 PP3 BP2 BP5 -

Apr 27, 2017

Illumina Laboratory Services, Illumina

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -

Nov 15, 2019

Natera, Inc.

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

Apr 16, 2022

Fulgent Genetics, Fulgent Genetics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not provided

Benign:3

Apr 07, 2020

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant is associated with the following publications: (PMID: 30341509, 33457257) -

Breakthrough Genomics, Breakthrough Genomics

Significance:Likely benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Jan 23, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not specified

Benign:1

Aug 24, 2015

Eurofins Ntd Llc (ga)

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.24

BayesDel_addAF

Benign

-0.21

BayesDel_noAF

Uncertain

-0.010

CADD

Benign

DANN

Uncertain

0.99

DEOGEN2

Pathogenic

0.88

Eigen

Benign

-0.34

Eigen_PC

Benign

-0.37

FATHMM_MKL

Uncertain

0.90

LIST_S2

Benign

0.79

MetaRNN

Benign

0.011

MetaSVM

Benign

-0.45

MutationAssessor

Pathogenic

3.1

PrimateAI

Benign

0.36

PROVEAN

Uncertain

-3.4

REVEL

Uncertain

0.61

Sift

Benign

0.089

Sift4G

Uncertain

0.040

Polyphen

0.45

Vest4

0.15

MPC

0.055

ClinPred

0.069

GERP RS

3.2

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.60

gMVP

0.92

Mutation Taster

=49/51

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

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