Genetic Variant NM_001079855.2:c.7+56C>G (chrX-2830251-C-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -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

Publications

6 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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 VariationId is 1294375.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001079855.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
GYG2	NM_001079855.2	MANE Select	c.7+56C>G	intron	N/A	NP_001073324.1	O15488-2
GYG2	NM_003918.3		c.7+56C>G	intron	N/A	NP_003909.2	O15488-1
GYG2	NM_001184702.2		c.7+56C>G	intron	N/A	NP_001171631.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
GYG2	ENST00000398806.8	TSL:1 MANE Select	c.7+56C>G	intron	N/A	ENSP00000381786.3	O15488-2
GYG2	ENST00000381163.7	TSL:1	c.7+56C>G	intron	N/A	ENSP00000370555.3	O15488-1
GYG2	ENST00000958345.1		c.7+56C>G	intron	N/A	ENSP00000628404.1

Frequencies

GnomAD3 genomes

AF:

0.688

AC:

76075

AN:

110503

Hom.:

19660

Cov.:

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

African (AFR)

AF:

0.397

AC:

9714

AN:

24445

American (AMR)

AF:

0.700

AC:

24286

AN:

34688

Ashkenazi Jewish (ASJ)

AF:

0.857

AC:

16006

AN:

18675

East Asian (EAS)

AF:

0.826

AC:

24476

AN:

29632

South Asian (SAS)

AF:

0.672

AC:

34616

AN:

51511

European-Finnish (FIN)

AF:

0.834

AC:

33638

AN:

40328

Middle Eastern (MID)

AF:

0.771

AC:

2929

AN:

3800

European-Non Finnish (NFE)

AF:

0.817

AC:

604891

AN:

740592

Other (OTH)

AF:

0.770

AC:

32546

AN:

42291

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

5017

10034

15051

20068

25085

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

15690

31380

47070

62760

78450

<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

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

African (AFR)

AF:

0.399

AC:

12135

AN:

30419

American (AMR)

AF:

0.737

AC:

7762

AN:

10531

Ashkenazi Jewish (ASJ)

AF:

0.863

AC:

2270

AN:

2631

East Asian (EAS)

AF:

0.818

AC:

2802

AN:

3426

South Asian (SAS)

AF:

0.649

AC:

1702

AN:

2623

European-Finnish (FIN)

AF:

0.836

AC:

4869

AN:

5826

Middle Eastern (MID)

AF:

0.734

AC:

157

AN:

214

European-Non Finnish (NFE)

AF:

0.813

AC:

42818

AN:

52698

Other (OTH)

AF:

0.702

AC:

1062

AN:

1513

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

734

1469

2203

2938

3672

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

660

1320

1980

2640

3300

<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:

0.740

Hom.:

5877

Bravo

AF:

0.671

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

2.6

(source)

DANN

Benign

0.19

PhyloP100

-0.88

PromoterAI

0.0030

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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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