rs6641656

Variant names:

• chrX-2830251-C-G
• rs6641656
• NM_001079855.2:c.7+56C>G

Your query was ambiguous. Multiple possible variants found:

• chrX-2830251-C-G
• chrX-2830251-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BP6_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
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.882
• Publications: 6 publications found

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]

ACMG classification

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	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.: 23

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

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

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

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

Alfa AF: 0.740 Hom.: 5877

Bravo AF: 0.671

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

Pathogenic	VUS	Benign	Condition
-	-	2	not provided (2)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.6
DANN	Benign	0.19
PhyloP100		-0.88
PromoterAI		0.0030	Neutral
Mutation Taster		=100/0	polymorphism (auto)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6641656;

hg19: chrX-2748292;

COSMIC: COSV58549930;