Genetic Variant NM_000642.3:c.207T>C (chr1-99861627-T-C) – ACMG Classification: Benign (-21 pts)

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2

The NM_000642.3(AGL):c.207T>C(p.Asn69Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0157 in 1,613,662 control chromosomes in the GnomAD database, including 249 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.015 ( 33 hom., cov: 32)

Exomes 𝑓: 0.016 ( 216 hom. )

Consequence

AGL
NM_000642.3 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:9

Conservation

PhyloP100: 0.572

Publications

6 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: Ambry Genetics, ClinGen, Orphanet, Labcorp Genetics (formerly Invitae), G2P, Genomics England PanelApp, Laboratory for Molecular Medicine, Myriad Women’s Health

AGL links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.52).

BP6

Variant 1-99861627-T-C is Benign according to our data. Variant chr1-99861627-T-C is described in ClinVar as Benign. ClinVar VariationId is 256726.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=0.572 with no splicing effect.

BS1

Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0152 (2309/152172) while in subpopulation NFE AF = 0.0185 (1258/68002). AF 95% confidence interval is 0.0176. There are 33 homozygotes in GnomAd4. There are 1156 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.

BS2

High Homozygotes in GnomAd4 at 33 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.207T>C	p.Asn69Asn	synonymous	Exon 3 of 34	NP_000633.2	P35573-1
AGL	NM_000028.3		c.207T>C	p.Asn69Asn	synonymous	Exon 3 of 34	NP_000019.2	P35573-1
AGL	NM_000643.3		c.207T>C	p.Asn69Asn	synonymous	Exon 3 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.207T>C	p.Asn69Asn	synonymous	Exon 3 of 34	ENSP00000355106.3	P35573-1
AGL	ENST00000294724.8	TSL:1	c.207T>C	p.Asn69Asn	synonymous	Exon 3 of 34	ENSP00000294724.4	P35573-1
AGL	ENST00000370163.7	TSL:1	c.207T>C	p.Asn69Asn	synonymous	Exon 3 of 34	ENSP00000359182.3	P35573-1

Frequencies

GnomAD3 genomes

AF:

0.0152

AC:

2311

AN:

152054

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00333

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0176

Gnomad ASJ

AF:

0.0398

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00394

Gnomad FIN

AF:

0.0393

Gnomad MID

AF:

0.0886

Gnomad NFE

AF:

0.0185

Gnomad OTH

AF:

0.0220

GnomAD2 exomes

AF:

0.0161

AC:

4043

AN:

251204

AF XY:

0.0160

show subpopulations

Gnomad AFR exome

AF:

0.00241

Gnomad AMR exome

AF:

0.00772

Gnomad ASJ exome

AF:

0.0415

Gnomad EAS exome

AF:

0.0000544

Gnomad FIN exome

AF:

0.0374

Gnomad NFE exome

AF:

0.0198

Gnomad OTH exome

AF:

0.0239

GnomAD4 exome

AF:

0.0157

AC:

23016

AN:

1461490

Hom.:

216

Cov.:

AF XY:

0.0156

AC XY:

11377

AN XY:

727070

show subpopulations

African (AFR)

AF:

0.00409

AC:

137

AN:

33456

American (AMR)

AF:

0.00850

AC:

380

AN:

44716

Ashkenazi Jewish (ASJ)

AF:

0.0423

AC:

1104

AN:

26126

East Asian (EAS)

AF:

0.0000252

AC:

AN:

39632

South Asian (SAS)

AF:

0.00417

AC:

360

AN:

86252

European-Finnish (FIN)

AF:

0.0383

AC:

2044

AN:

53416

Middle Eastern (MID)

AF:

0.0470

AC:

271

AN:

5762

European-Non Finnish (NFE)

AF:

0.0159

AC:

17648

AN:

1111748

Other (OTH)

AF:

0.0177

AC:

1071

AN:

60382

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.481

Heterozygous variant carriers

1237

2474

3712

4949

6186

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

612

1224

1836

2448

3060

<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:

0.0152

AC:

2309

AN:

152172

Hom.:

Cov.:

AF XY:

0.0155

AC XY:

1156

AN XY:

74398

show subpopulations

African (AFR)

AF:

0.00332

AC:

138

AN:

41532

American (AMR)

AF:

0.0175

AC:

268

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.0398

AC:

138

AN:

3466

East Asian (EAS)

AF:

0.00

AC:

AN:

5180

South Asian (SAS)

AF:

0.00394

AC:

AN:

4818

European-Finnish (FIN)

AF:

0.0393

AC:

416

AN:

10576

Middle Eastern (MID)

AF:

0.0884

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0185

AC:

1258

AN:

68002

Other (OTH)

AF:

0.0218

AC:

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

112

223

335

446

558

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

104

130

<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:

0.0174

Hom.:

Bravo

AF:

0.0128

Asia WGS

AF:

0.00462

AC:

AN:

3478

EpiCase

AF:

0.0194

EpiControl

AF:

0.0187

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

Glycogen storage disease type III (4)

not provided (3)

not specified (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.52

CADD

Benign

5.3

(source)

DANN

Benign

0.65

PhyloP100

0.57

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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