Genetic Variant GYG1:c.481+178_481+179delGT (chr3-148997054-TTG-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_004130.4(GYG1):c.481+178_481+179delGT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.237 in 595,546 control chromosomes in the GnomAD database, including 7,736 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.25 ( 4893 hom., cov: 0)

Exomes 𝑓: 0.23 ( 2843 hom. )

Consequence

GYG1
NM_004130.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.285

Variant links:

Genes affected

GYG1 (HGNC:4699): (glycogenin 1) This gene encodes a member of the glycogenin family. Glycogenin is a glycosyltransferase that catalyzes the formation of a short glucose polymer from uridine diphosphate glucose in an autoglucosylation reaction. This reaction is followed by elongation and branching of the polymer, catalyzed by glycogen synthase and branching enzyme, to form glycogen. This gene is expressed in muscle and other tissues. Mutations in this gene result in glycogen storage disease XV. This gene has pseudogenes on chromosomes 1, 8 and 13 respectively. Alternatively spliced transcript variants encoding different isoforms have been identified.[provided by RefSeq, Sep 2010]

GYG1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 3-148997054-TTG-T is Benign according to our data. Variant chr3-148997054-TTG-T is described in ClinVar as [Benign]. Clinvar id is 1240865.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.385 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
GYG1	NM_004130.4 link	c.481+178_481+179delGT	intron_variant	Intron 4 of 7	ENST00000345003.9	NP_004121.2	P46976-1
GYG1	NM_001184720.2 link	c.481+178_481+179delGT	intron_variant	Intron 4 of 6		NP_001171649.1	P46976-2
GYG1	NM_001184721.2 link	c.481+178_481+179delGT	intron_variant	Intron 4 of 5		NP_001171650.1	P46976-3
GYG1	XM_017006275.2 link	c.304+178_304+179delGT	intron_variant	Intron 3 of 5		XP_016861764.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GYG1	ENST00000345003.9 link	c.481+151_481+152delTG		intron_variant	Intron 4 of 7	1	NM_004130.4	ENSP00000340736.4		P46976-1

Frequencies

GnomAD3 genomes

AF:

0.254

AC:

37945

AN:

149440

Hom.:

4890

Cov.:

show subpopulations

Gnomad AFR

AF:

0.274

Gnomad AMI

AF:

0.346

Gnomad AMR

AF:

0.309

Gnomad ASJ

AF:

0.270

Gnomad EAS

AF:

0.399

Gnomad SAS

AF:

0.216

Gnomad FIN

AF:

0.179

Gnomad MID

AF:

0.315

Gnomad NFE

AF:

0.229

Gnomad OTH

AF:

0.287

GnomAD4 exome

AF:

0.231

AC:

102927

AN:

445990

Hom.:

2843

AF XY:

0.228

AC XY:

54222

AN XY:

238066

show subpopulations

Gnomad4 AFR exome

AF:

0.231

Gnomad4 AMR exome

AF:

0.242

Gnomad4 ASJ exome

AF:

0.232

Gnomad4 EAS exome

AF:

0.359

Gnomad4 SAS exome

AF:

0.203

Gnomad4 FIN exome

AF:

0.188

Gnomad4 NFE exome

AF:

0.224

Gnomad4 OTH exome

AF:

0.242

GnomAD4 genome

AF:

0.254

AC:

37980

AN:

149556

Hom.:

4893

Cov.:

AF XY:

0.255

AC XY:

18584

AN XY:

72968

show subpopulations

Gnomad4 AFR

AF:

0.274

Gnomad4 AMR

AF:

0.309

Gnomad4 ASJ

AF:

0.270

Gnomad4 EAS

AF:

0.399

Gnomad4 SAS

AF:

0.216

Gnomad4 FIN

AF:

0.179

Gnomad4 NFE

AF:

0.229

Gnomad4 OTH

AF:

0.286

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Sep 24, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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.

3-148997054-TTGTGTGTGTGTGTG-TTGTGTGTGTGTG

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