Genetic Variant AGL:p.Ser841Phe (chr1-99884427-C-T) – ACMG Classification: Benign (-20 pts)

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The NM_000642.3(AGL):c.2522C>T(p.Ser841Phe) variant causes a missense change. The variant allele was found at a frequency of 0.00204 in 1,612,178 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts 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. S841Y) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.0023 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0020 ( 10 hom. )

Consequence

AGL
NM_000642.3 missense

Scores

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:9

Conservation

PhyloP100: 5.68

Publications

7 publications found

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 Gene-Disease associations (from GenCC):

glycogen storage disease III
Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Laboratory for Molecular Medicine, Myriad Women's Health, Genomics England PanelApp, G2P, ClinGen, Orphanet, Labcorp Genetics (formerly Invitae), Ambry Genetics

AGL links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_000642.3, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.010740131).

BP6

Variant 1-99884427-C-T is Benign according to our data. Variant chr1-99884427-C-T is described in ClinVar as Benign/Likely_benign. ClinVar VariationId is 256727.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.00228 (346/151948) while in subpopulation AMR AF = 0.0036 (55/15266). AF 95% confidence interval is 0.00284. There are 2 homozygotes in GnomAd4. There are 158 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000642.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
AGL	NM_000642.3	MANE Select	c.2522C>T	p.Ser841Phe	missense	Exon 19 of 34	NP_000633.2	P35573-1
AGL	NM_000028.3		c.2522C>T	p.Ser841Phe	missense	Exon 19 of 34	NP_000019.2	P35573-1
AGL	NM_000643.3		c.2522C>T	p.Ser841Phe	missense	Exon 19 of 34	NP_000634.2	A0A0S2A4E4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
AGL	ENST00000361915.8	TSL:1 MANE Select	c.2522C>T	p.Ser841Phe	missense	Exon 19 of 34	ENSP00000355106.3	P35573-1
AGL	ENST00000294724.8	TSL:1	c.2522C>T	p.Ser841Phe	missense	Exon 19 of 34	ENSP00000294724.4	P35573-1
AGL	ENST00000370163.7	TSL:1	c.2522C>T	p.Ser841Phe	missense	Exon 19 of 34	ENSP00000359182.3	P35573-1

Frequencies

GnomAD3 genomes

AF:

0.00228

AC:

346

AN:

151830

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000291

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00361

Gnomad ASJ

AF:

0.0141

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00352

Gnomad FIN

AF:

0.000380

Gnomad MID

AF:

0.0348

Gnomad NFE

AF:

0.00271

Gnomad OTH

AF:

0.00671

GnomAD2 exomes

AF:

0.00277

AC:

689

AN:

248886

AF XY:

0.00300

show subpopulations

Gnomad AFR exome

AF:

0.000257

Gnomad AMR exome

AF:

0.00183

Gnomad ASJ exome

AF:

0.0151

Gnomad EAS exome

AF:

0.0000546

Gnomad FIN exome

AF:

0.000186

Gnomad NFE exome

AF:

0.00307

Gnomad OTH exome

AF:

0.00512

GnomAD4 exome

AF:

0.00201

AC:

2938

AN:

1460230

Hom.:

Cov.:

AF XY:

0.00217

AC XY:

1576

AN XY:

726484

show subpopulations

African (AFR)

AF:

0.00123

AC:

AN:

33416

American (AMR)

AF:

0.00199

AC:

AN:

44634

Ashkenazi Jewish (ASJ)

AF:

0.0150

AC:

392

AN:

26118

East Asian (EAS)

AF:

0.0000252

AC:

AN:

39614

South Asian (SAS)

AF:

0.00326

AC:

281

AN:

86176

European-Finnish (FIN)

AF:

0.000301

AC:

AN:

53174

Middle Eastern (MID)

AF:

0.0186

AC:

107

AN:

5758

European-Non Finnish (NFE)

AF:

0.00161

AC:

1791

AN:

1111022

Other (OTH)

AF:

0.00365

AC:

220

AN:

60318

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.473

Heterozygous variant carriers

145

291

436

582

727

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

128

192

256

320

<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:

0.00228

AC:

346

AN:

151948

Hom.:

Cov.:

AF XY:

0.00213

AC XY:

158

AN XY:

74268

show subpopulations

African (AFR)

AF:

0.000314

AC:

AN:

41406

American (AMR)

AF:

0.00360

AC:

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.0141

AC:

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5178

South Asian (SAS)

AF:

0.00353

AC:

AN:

4822

European-Finnish (FIN)

AF:

0.000380

AC:

AN:

10536

Middle Eastern (MID)

AF:

0.0340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00271

AC:

184

AN:

67956

Other (OTH)

AF:

0.00664

AC:

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.508

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<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:

0.00274

Hom.:

Bravo

AF:

0.00221

Asia WGS

AF:

0.00260

AC:

AN:

3478

EpiCase

AF:

0.00404

EpiControl

AF:

0.00457

ClinVar

ClinVar submissions

Significance:Benign/Likely benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

Glycogen storage disease type III (3)

not provided (3)

AGL-related disorder (1)

Inborn genetic diseases (1)

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.21

BayesDel_addAF

Benign

-0.45

BayesDel_noAF

Benign

-0.42

CADD

Uncertain

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.11

Eigen

Uncertain

0.24

Eigen_PC

Uncertain

0.41

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Pathogenic

0.97

M_CAP

Benign

0.035

MetaRNN

Benign

0.011

MetaSVM

Benign

-1.1

MutationAssessor

Benign

1.1

PhyloP100

5.7

PrimateAI

Benign

0.46

PROVEAN

Benign

-2.2

REVEL

Benign

0.084

Sift

Benign

0.031

Sift4G

Uncertain

0.051

Varity_R

0.46

gMVP

0.69

Mutation Taster

=100/0

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

Details are displayed if max score is > 0.2

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over