NM_206809.4:c.593-348C>G

Variant names:

• chr6-29669933-C-G
• rs3095291
• NM_206809.4:c.593-348C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_206809.4(MOG):​c.593-348C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.807 in 152,006 control chromosomes in the GnomAD database, including 49,721 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 0.81 (49721 hom., cov: 30)
• Consequence: MOG NM_206809.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.315
• Publications: 3 publications found

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]

MOG Gene-Disease associations (from GenCC):

• narcolepsy 7

  Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.846 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_206809.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MOG	NM_206809.4	MANE Select	c.593-348C>G		intron	N/A	NP_996532.2
	MOG	NM_001363610.2		c.593-348C>G		intron	N/A	NP_001350539.1
	MOG	NM_002433.5		c.593-348C>G		intron	N/A	NP_002424.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MOG	ENST00000376917.8	TSL:1 MANE Select	c.593-348C>G		intron	N/A	ENSP00000366115.3
	MOG	ENST00000376894.8	TSL:1	c.593-348C>G		intron	N/A	ENSP00000366091.4
	MOG	ENST00000376898.7	TSL:1	c.593-348C>G		intron	N/A	ENSP00000366095.3

Frequencies

GnomAD3 genomes AF: 0.807 AC: 122539 AN: 151892 Hom.: 49673 Cov.: 30

Gnomad AFR AF: 0.838

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.858

Gnomad ASJ AF: 0.822

Gnomad EAS AF: 0.856

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.794

Gnomad NFE AF: 0.794

Gnomad OTH AF: 0.811

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

GnomAD4 genome AF: 0.807 AC: 122644 AN: 152006 Hom.: 49721 Cov.: 30 AF XY: 0.803 AC XY: 59658 AN XY: 74282

African (AFR) AF: 0.837 AC: 34734 AN: 41474

American (AMR) AF: 0.858 AC: 13116 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.822 AC: 2850 AN: 3468

East Asian (EAS) AF: 0.856 AC: 4414 AN: 5154

South Asian (SAS) AF: 0.826 AC: 3970 AN: 4808

European-Finnish (FIN) AF: 0.656 AC: 6904 AN: 10524

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.794 AC: 54000 AN: 67990

Other (OTH) AF: 0.813 AC: 1709 AN: 2102

Alfa AF: 0.761 Hom.: 2597

Bravo AF: 0.824

Asia WGS AF: 0.855 AC: 2973 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.81
PhyloP100		-0.32
Mutation Taster		=100/0	polymorphism (auto)

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: rs3095291; hg19: chr6-29637710;