X-2830251-C-G

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

2

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]

Genome browser will be placed here

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
GYG2NM_001079855.2 linkc.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
GYG2ENST00000398806.8 linkc.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.:
23
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.:
23
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.

Other links and lift over

dbSNP: rs6641656; hg19: chrX-2748292; COSMIC: COSV58549930; API