rs12043139

Positions:

chr1-99910769-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_000642.3(AGL):c.3758G>A(p.Arg1253His) variant causes a missense change. The variant allele was found at a frequency of 0.0021 in 1,612,440 control chromosomes in the GnomAD database, including 34 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1253C) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.0053 ( 5 hom., cov: 32)

Exomes 𝑓: 0.0018 ( 29 hom. )

Consequence

AGL
NM_000642.3 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 3.93

Variant links:

Genes affected

AGL (HGNC:321): (amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase) This gene encodes the glycogen debrancher enzyme which is involved in glycogen degradation. This enzyme has two independent catalytic activities which occur at different sites on the protein: a 4-alpha-glucotransferase activity and a amylo-1,6-glucosidase activity. Mutations in this gene are associated with glycogen storage disease although a wide range of enzymatic and clinical variability occurs which may be due to tissue-specific alternative splicing. Alternatively spliced transcripts encoding different isoforms have been described. [provided by RefSeq, Jul 2008]

AGL links:

AGL (HGNC:):

AGL 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 (MetaRNN=0.0062305927).

BP6

Variant 1-99910769-G-A is Benign according to our data. Variant chr1-99910769-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 256743.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0053 (806/152156) while in subpopulation EAS AF= 0.0347 (180/5188). AF 95% confidence interval is 0.0306. There are 5 homozygotes in gnomad4. There are 409 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 5 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AGL	NM_000642.3 linkuse as main transcript	c.3758G>A	p.Arg1253His	missense_variant	28/34	ENST00000361915.8	NP_000633.2	P35573-1A0A0S2A4E4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AGL	ENST00000361915.8 linkuse as main transcript	c.3758G>A	p.Arg1253His	missense_variant	28/34	1	NM_000642.3	ENSP00000355106.3		P35573-1

Frequencies

GnomAD3 genomes

AF:

0.00529

AC:

805

AN:

152040

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0120

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00184

Gnomad ASJ

AF:

0.000865

Gnomad EAS

AF:

0.0344

Gnomad SAS

AF:

0.00207

Gnomad FIN

AF:

0.00491

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000427

Gnomad OTH

AF:

0.00431

GnomAD3 exomes

AF:

0.00493

AC:

1237

AN:

250934

Hom.:

AF XY:

0.00425

AC XY:

576

AN XY:

135614

show subpopulations

Gnomad AFR exome

AF:

0.0121

Gnomad AMR exome

AF:

0.000637

Gnomad ASJ exome

AF:

0.000298

Gnomad EAS exome

AF:

0.0339

Gnomad SAS exome

AF:

0.00311

Gnomad FIN exome

AF:

0.00587

Gnomad NFE exome

AF:

0.00131

Gnomad OTH exome

AF:

0.00343

GnomAD4 exome

AF:

0.00177

AC:

2587

AN:

1460284

Hom.:

Cov.:

AF XY:

0.00165

AC XY:

1202

AN XY:

726496

show subpopulations

Gnomad4 AFR exome

AF:

0.0114

Gnomad4 AMR exome

AF:

0.000895

Gnomad4 ASJ exome

AF:

0.000115

Gnomad4 EAS exome

AF:

0.0199

Gnomad4 SAS exome

AF:

0.00262

Gnomad4 FIN exome

AF:

0.00611

Gnomad4 NFE exome

AF:

0.000449

Gnomad4 OTH exome

AF:

0.00525

GnomAD4 genome

AF:

0.00530

AC:

806

AN:

152156

Hom.:

Cov.:

AF XY:

0.00550

AC XY:

409

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.0119

Gnomad4 AMR

AF:

0.00183

Gnomad4 ASJ

AF:

0.000865

Gnomad4 EAS

AF:

0.0347

Gnomad4 SAS

AF:

0.00207

Gnomad4 FIN

AF:

0.00491

Gnomad4 NFE

AF:

0.000427

Gnomad4 OTH

AF:

0.00427

Alfa

AF:

0.00186

Hom.:

Bravo

AF:

0.00562

ESP6500AA

AF:

0.0102

AC:

ESP6500EA

AF:

0.000930

AC:

ExAC

AF:

0.00530

AC:

644

Asia WGS

AF:

0.0250

AC:

AN:

3476

EpiCase

AF:

0.0000545

EpiControl

AF:

0.000356

ClinVar

Significance: Benign/Likely benign

Submissions summary: Benign:8

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Glycogen storage disease type III

Benign:5

Likely benign, criteria provided, single submitter	clinical testing	Phosphorus, Inc.	Aug 01, 2017	- -
Benign, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Jan 13, 2018	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Jul 15, 2021	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
Benign, no assertion criteria provided	clinical testing	Natera, Inc.	Sep 16, 2020	- -

not specified

Benign:2

Benign, criteria provided, single submitter	clinical testing	PreventionGenetics, part of Exact Sciences	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Dec 28, 2016	This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Oct 13, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.13

BayesDel_addAF

Benign

-0.44

BayesDel_noAF

Benign

-0.37

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.054

T;T;T;T;.

Eigen

Benign

-0.073

Eigen_PC

Benign

0.027

FATHMM_MKL

Uncertain

0.94

LIST_S2

Uncertain

0.91

D;.;.;.;D

MetaRNN

Benign

0.0062

T;T;T;T;T

MetaSVM

Benign

-0.88

MutationAssessor

Uncertain

2.3

M;M;M;M;.

PrimateAI

Benign

0.42

PROVEAN

Benign

-1.1

N;N;N;N;N

REVEL

Benign

0.094

Sift

Benign

0.074

T;T;T;T;T

Sift4G

Benign

0.10

T;T;T;T;T

Polyphen

0.29

B;B;B;B;B

Vest4

0.28

MVP

0.73

MPC

0.049

ClinPred

0.018

GERP RS

2.4

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.032

gMVP

0.84

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