10-101800564-T-C

Position:

• chr10-101800564-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_012215.5(OGA):​c.1037-164A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 152,008 control chromosomes in the GnomAD database, including 6,775 homozygotes. 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: 𝑓 0.29 (6775 hom., cov: 32)
• Consequence: OGA NM_012215.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.659

Genes affected

OGA (HGNC:7056): (O-GlcNAcase) The dynamic modification of cytoplasmic and nuclear proteins by O-linked N-acetylglucosamine (O-GlcNAc) addition and removal on serine and threonine residues is catalyzed by OGT (MIM 300255), which adds O-GlcNAc, and MGEA5, a glycosidase that removes O-GlcNAc modifications (Gao et al., 2001 [PubMed 11148210]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
OGA	NM_012215.5	c.1037-164A>G		intron_variant		ENST00000361464.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
OGA	ENST00000361464.8	c.1037-164A>G		intron_variant		1	NM_012215.5	P2
OGA	ENST00000357797.9	c.1037-1109A>G		intron_variant		1		A2
OGA	ENST00000370094.7	c.1037-164A>G		intron_variant		1
OGA	ENST00000439817.5	c.1037-1109A>G		intron_variant		5		A2

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43805 AN: 151890 Hom.: 6760 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.289

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.288 AC: 43845 AN: 152008 Hom.: 6775 Cov.: 32 AF XY: 0.288 AC XY: 21356 AN XY: 74276

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.308

Gnomad4 ASJ AF: 0.266

Gnomad4 EAS AF: 0.239

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.296

Alfa AF: 0.328 Hom.: 1679

Bravo AF: 0.282

Asia WGS AF: 0.186 AC: 650 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	14
DANN	Benign	0.75

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

LitVar

Other links and lift over

dbSNP: rs2305192; hg19: chr10-103560321;