rs1318631

chr6-29667731-G-A

Variant summary

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

The NM_206809.4(MOG):c.571+68G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 1,587,292 control chromosomes in the GnomAD database, including 39,764 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 0.19 (3162 hom., cov: 32)
  • Exomes 𝑓: 0.22 (36602 hom.)
• Consequence: MOG NM_206809.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.19

Genes affected

MOG (HGNC:7197): (myelin oligodendrocyte glycoprotein) The product of this gene is a membrane protein expressed on the oligodendrocyte cell surface and the outermost surface of myelin sheaths. Due to this localization, it is a primary target antigen involved in immune-mediated demyelination. This protein may be involved in completion and maintenance of the myelin sheath and in cell-cell communication. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MOG	NM_206809.4	c.571+68G>A		intron_variant		ENST00000376917.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MOG	ENST00000376917.8	c.571+68G>A		intron_variant		1	NM_206809.4	P1

Frequencies

GnomAD3 genomes AF: 0.194 AC: 29541 AN: 152004 Hom.: 3161 Cov.: 32

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.266

Gnomad AMR AF: 0.184

Gnomad ASJ AF: 0.158

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.159

GnomAD4 exome AF: 0.220 AC: 316370 AN: 1435170 Hom.: 36602 Cov.: 27 AF XY: 0.217 AC XY: 155472 AN XY: 715724

Gnomad4 AFR exome AF: 0.107

Gnomad4 AMR exome AF: 0.238

Gnomad4 ASJ exome AF: 0.156

Gnomad4 EAS exome AF: 0.267

Gnomad4 SAS exome AF: 0.104

Gnomad4 FIN exome AF: 0.301

Gnomad4 NFE exome AF: 0.230

Gnomad4 OTH exome AF: 0.202

GnomAD4 genome AF: 0.194 AC: 29547 AN: 152122 Hom.: 3162 Cov.: 32 AF XY: 0.195 AC XY: 14493 AN XY: 74362

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.184

Gnomad4 ASJ AF: 0.158

Gnomad4 EAS AF: 0.273

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.158

Alfa AF: 0.217 Hom.: 4087

Bravo AF: 0.186

Asia WGS AF: 0.164 AC: 570 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.41
Dann	Benign	0.66

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: rs1318631; hg19: chr6-29635508; COSMIC: COSV65307022; COSMIC: COSV65307022;