Genetic Variant GYG2:c.8-229dupT (chrX-2842979-A-AT) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP6_Moderate

The NM_001079855.2(GYG2):c.8-229dupT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000915 in 109,282 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. Variant has been reported in ClinVar as Benign (★). There are indicators that this mutation may affect the branch point..

Frequency

Genomes: 𝑓 0.0000092 ( 0 hom., 1 hem., cov: 21)

Exomes 𝑓: 0.0000095 ( 0 hom. 1 hem. )

Failed GnomAD Quality Control

Consequence

GYG2
NM_001079855.2 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0130

Publications

0 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: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP6

Variant X-2842979-A-AT is Benign according to our data. Variant chrX-2842979-A-AT is described in ClinVar as Benign. ClinVar VariationId is 1944675.Status of the report is criteria_provided_single_submitter, 1 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.8-229dupT	intron	N/A	NP_001073324.1	O15488-2
GYG2	NM_003918.3		c.8-14dupT	intron	N/A	NP_003909.2	O15488-1
GYG2	NM_001184702.2		c.8-229dupT	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.8-234_8-233insT	intron	N/A	ENSP00000381786.3	O15488-2
GYG2	ENST00000381163.7	TSL:1	c.8-19_8-18insT	intron	N/A	ENSP00000370555.3	O15488-1
GYG2	ENST00000958345.1		c.8-19_8-18insT	intron	N/A	ENSP00000628404.1

Frequencies

GnomAD3 genomes

AF:

0.00000915

AC:

AN:

109282

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000191

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00000945

AC:

AN:

317420

Hom.:

Cov.:

AF XY:

0.0000103

AC XY:

AN XY:

97500

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

10635

American (AMR)

AF:

0.00

AC:

AN:

22105

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

10623

East Asian (EAS)

AF:

0.00

AC:

AN:

19024

South Asian (SAS)

AF:

0.0000322

AC:

AN:

31018

European-Finnish (FIN)

AF:

0.00

AC:

AN:

19872

Middle Eastern (MID)

AF:

0.000730

AC:

AN:

1369

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

184322

Other (OTH)

AF:

0.0000542

AC:

AN:

18452

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.00000915

AC:

AN:

109282

Hom.:

Cov.:

AF XY:

0.0000316

AC XY:

AN XY:

31676

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

29959

American (AMR)

AF:

0.00

AC:

AN:

10175

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2608

East Asian (EAS)

AF:

0.00

AC:

AN:

3478

South Asian (SAS)

AF:

0.00

AC:

AN:

2480

European-Finnish (FIN)

AF:

0.00

AC:

AN:

5746

Middle Eastern (MID)

AF:

0.00

AC:

AN:

234

European-Non Finnish (NFE)

AF:

0.0000191

AC:

AN:

52472

Other (OTH)

AF:

0.00

AC:

AN:

1458

Age Distribution

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:

0.00

Hom.:

Bravo

AF:

0.00000756

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.013

La Branchor

0.74

BranchPoint Hunter

7.0

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over