X-2842935-T-A

Variant names:

• chrX-2842935-T-A
• rs5982883
• NM_001079855.2:c.8-278T>A

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_001079855.2(GYG2):​c.8-278T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000307 in 227,972 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 20)
  • Exomes 𝑓: 0.000031 (0 hom. 2 hem.)
• Consequence: GYG2 NM_001079855.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.554
• Publications: 1 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 -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BS2: High Hemizygotes in GnomAdExome4 at 2 gene

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.8-278T>A		intron	N/A	NP_001073324.1	O15488-2
	GYG2	NM_003918.3		c.8-63T>A		intron	N/A	NP_003909.2	O15488-1
	GYG2	NM_001184702.2		c.8-278T>A		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.8-278T>A		intron	N/A	ENSP00000381786.3	O15488-2
	GYG2	ENST00000381163.7	TSL:1	c.8-63T>A		intron	N/A	ENSP00000370555.3	O15488-1
	GYG2	ENST00000958345.1		c.8-63T>A		intron	N/A	ENSP00000628404.1

Frequencies

GnomAD3 genomes Cov.: 20

GnomAD4 exome AF: 0.0000307 AC: 7 AN: 227972 Hom.: 0 AF XY: 0.0000279 AC XY: 2 AN XY: 71770

African (AFR) AF: 0.00 AC: 0 AN: 7638

American (AMR) AF: 0.00 AC: 0 AN: 16095

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 6720

East Asian (EAS) AF: 0.000496 AC: 6 AN: 12098

South Asian (SAS) AF: 0.00 AC: 0 AN: 27984

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 12086

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 842

European-Non Finnish (NFE) AF: 0.00000759 AC: 1 AN: 131831

Other (OTH) AF: 0.00 AC: 0 AN: 12678

GnomAD4 genome Cov.: 20

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.1
DANN	Benign	0.91
PhyloP100		-0.55
PromoterAI		0.0044	Neutral

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

Other links and lift over

dbSNP: rs5982883; hg19: chrX-2760976;