Genetic Variant NM_001079855.2:c.7+17G>C (chrX-2830212-G-C) – 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+17G>C 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 0.93 ( 34060 hom., 31572 hem., cov: 24)

Exomes 𝑓: 0.98 ( 355467 hom. 351214 hem. )

Failed GnomAD Quality Control

Consequence

GYG2
NM_001079855.2 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -1.88

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=-0.98).

BP6

Variant X-2830212-G-C is Benign according to our data. Variant chrX-2830212-G-C is described in ClinVar as Benign. ClinVar VariationId is 379979.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+17G>C	intron	N/A	NP_001073324.1	O15488-2
GYG2	NM_003918.3		c.7+17G>C	intron	N/A	NP_003909.2	O15488-1
GYG2	NM_001184702.2		c.7+17G>C	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+17G>C	intron	N/A	ENSP00000381786.3	O15488-2
GYG2	ENST00000381163.7	TSL:1	c.7+17G>C	intron	N/A	ENSP00000370555.3	O15488-1
GYG2	ENST00000958345.1		c.7+17G>C	intron	N/A	ENSP00000628404.1

Frequencies

GnomAD3 genomes

AF:

0.934

AC:

104045

AN:

111384

Hom.:

34069

Cov.:

show subpopulations

Gnomad AFR

AF:

0.811

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.911

Gnomad ASJ

AF:

0.992

Gnomad EAS

AF:

0.989

Gnomad SAS

AF:

0.979

Gnomad FIN

AF:

0.989

Gnomad MID

AF:

0.975

Gnomad NFE

AF:

0.994

Gnomad OTH

AF:

0.933

GnomAD2 exomes

AF:

0.956

AC:

172597

AN:

180480

AF XY:

0.968

show subpopulations

Gnomad AFR exome

AF:

0.810

Gnomad AMR exome

AF:

0.852

Gnomad ASJ exome

AF:

0.993

Gnomad EAS exome

AF:

0.988

Gnomad FIN exome

AF:

0.991

Gnomad NFE exome

AF:

0.994

Gnomad OTH exome

AF:

0.971

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff

AF:

0.984

AC:

1072756

AN:

1089857

Hom.:

355467

Cov.:

AF XY:

0.986

AC XY:

351214

AN XY:

356293

show subpopulations

African (AFR)

AF:

0.813

AC:

21337

AN:

26256

American (AMR)

AF:

0.861

AC:

30215

AN:

35111

Ashkenazi Jewish (ASJ)

AF:

0.992

AC:

19180

AN:

19325

East Asian (EAS)

AF:

0.990

AC:

29836

AN:

30148

South Asian (SAS)

AF:

0.981

AC:

52930

AN:

53937

European-Finnish (FIN)

AF:

0.992

AC:

40178

AN:

40520

Middle Eastern (MID)

AF:

0.983

AC:

4043

AN:

4113

European-Non Finnish (NFE)

AF:

0.995

AC:

830422

AN:

834655

Other (OTH)

AF:

0.974

AC:

44615

AN:

45792

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.460

Heterozygous variant carriers

532

1064

1595

2127

2659

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

21204

42408

63612

84816

106020

<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:

0.934

AC:

104083

AN:

111438

Hom.:

34060

Cov.:

AF XY:

0.938

AC XY:

31572

AN XY:

33642

show subpopulations

African (AFR)

AF:

0.811

AC:

24826

AN:

30602

American (AMR)

AF:

0.911

AC:

9679

AN:

10623

Ashkenazi Jewish (ASJ)

AF:

0.992

AC:

2629

AN:

2650

East Asian (EAS)

AF:

0.989

AC:

3446

AN:

3484

South Asian (SAS)

AF:

0.978

AC:

2593

AN:

2650

European-Finnish (FIN)

AF:

0.989

AC:

5933

AN:

6001

Middle Eastern (MID)

AF:

0.972

AC:

210

AN:

216

European-Non Finnish (NFE)

AF:

0.994

AC:

52666

AN:

53010

Other (OTH)

AF:

0.933

AC:

1417

AN:

1518

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

232

465

697

930

1162

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

832

1664

2496

3328

4160

<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:

0.966

Hom.:

13096

Bravo

AF:

0.921

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, multiple submitters, no conflicts

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (2)

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

2.8

(source)

DANN

Benign

0.35

PhyloP100

-1.9

PromoterAI

-0.020

Neutral

(source)

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