Genetic Variant GYG2:c.7+56C>G (chrX-2830251-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBP6_Very_Strong

The NM_001079855.2(GYG2):c.7+56C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.69 ( 19648 hom., 22707 hem., cov: 23)

Exomes 𝑓: 0.79 ( 219546 hom. 234530 hem. )

Failed GnomAD Quality Control

Consequence

GYG2
NM_001079855.2 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.882

Variant links:

Genes affected

GYG2 (HGNC:4700): (glycogenin 2) This gene encodes a member of the the glycogenin family. Glycogenin is a self-glucosylating protein involved in the initiation reactions of glycogen biosynthesis. A gene on chromosome 3 encodes the muscle glycogenin and this X-linked gene encodes the glycogenin mainly present in liver; both are involved in blood glucose homeostasis. This gene has a short version on chromosome Y, which is 3' truncated and can not make a functional protein. Multiple alternatively spliced transcript variants encoding different isoforms have been identified.[provided by RefSeq, May 2010]

GYG2 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.99).

BP6

Variant X-2830251-C-G is Benign according to our data. Variant chrX-2830251-C-G is described in ClinVar as [Benign]. Clinvar id is 1294375.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GYG2	NM_001079855.2 link	c.7+56C>G		intron_variant	Intron 2 of 10	ENST00000398806.8	NP_001073324.1	O15488-2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GYG2	ENST00000398806.8 link	c.7+56C>G		intron_variant	Intron 2 of 10	1	NM_001079855.2	ENSP00000381786.3		O15488-2

Frequencies

GnomAD3 genomes

AF:

0.688

AC:

76075

AN:

110503

Hom.:

19660

Cov.:

AF XY:

0.692

AC XY:

22686

AN XY:

32783

show subpopulations

Gnomad AFR

AF:

0.399

Gnomad AMI

AF:

0.744

Gnomad AMR

AF:

0.737

Gnomad ASJ

AF:

0.863

Gnomad EAS

AF:

0.818

Gnomad SAS

AF:

0.649

Gnomad FIN

AF:

0.836

Gnomad MID

AF:

0.740

Gnomad NFE

AF:

0.813

Gnomad OTH

AF:

0.705

GnomAD4 exome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.794

AC:

783102

AN:

985962

Hom.:

219546

AF XY:

0.799

AC XY:

234530

AN XY:

293632

show subpopulations

Gnomad4 AFR exome

AF:

0.397

Gnomad4 AMR exome

AF:

0.700

Gnomad4 ASJ exome

AF:

0.857

Gnomad4 EAS exome

AF:

0.826

Gnomad4 SAS exome

AF:

0.672

Gnomad4 FIN exome

AF:

0.834

Gnomad4 NFE exome

AF:

0.817

Gnomad4 OTH exome

AF:

0.770

GnomAD4 genome

Data not reliable, filtered out with message: InbreedingCoeff

AF:

0.688

AC:

76079

AN:

110556

Hom.:

19648

Cov.:

AF XY:

0.691

AC XY:

22707

AN XY:

32846

show subpopulations

Gnomad4 AFR

AF:

0.399

Gnomad4 AMR

AF:

0.737

Gnomad4 ASJ

AF:

0.863

Gnomad4 EAS

AF:

0.818

Gnomad4 SAS

AF:

0.649

Gnomad4 FIN

AF:

0.836

Gnomad4 NFE

AF:

0.813

Gnomad4 OTH

AF:

0.702

Alfa

AF:

0.740

Hom.:

5877

Bravo

AF:

0.671

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jun 23, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

2.6

DANN

Benign

0.19

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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