6-29660660-T-C

Position:

• chr6-29660660-T-C

Variant summary

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

The NM_206809.4(MOG):​c.436+994T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.876 in 147,944 control chromosomes in the GnomAD database, including 57,222 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 0.88 (57222 hom., cov: 25)
• Consequence: MOG NM_206809.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.399

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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.954 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MOG	NM_206809.4	c.436+994T>C		intron_variant		ENST00000376917.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MOG	ENST00000376917.8	c.436+994T>C		intron_variant		1	NM_206809.4	P1

Frequencies

GnomAD3 genomes AF: 0.876 AC: 129460 AN: 147834 Hom.: 57157 Cov.: 25

Gnomad AFR AF: 0.955

Gnomad AMI AF: 0.848

Gnomad AMR AF: 0.913

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.977

Gnomad SAS AF: 0.925

Gnomad FIN AF: 0.684

Gnomad MID AF: 0.876

Gnomad NFE AF: 0.837

Gnomad OTH AF: 0.886

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

GnomAD4 genome AF: 0.876 AC: 129581 AN: 147944 Hom.: 57222 Cov.: 25 AF XY: 0.872 AC XY: 62580 AN XY: 71744

Gnomad4 AFR AF: 0.956

Gnomad4 AMR AF: 0.913

Gnomad4 ASJ AF: 0.875

Gnomad4 EAS AF: 0.977

Gnomad4 SAS AF: 0.926

Gnomad4 FIN AF: 0.684

Gnomad4 NFE AF: 0.837

Gnomad4 OTH AF: 0.888

Alfa AF: 0.851 Hom.: 50511

Bravo AF: 0.896

Asia WGS AF: 0.949 AC: 3302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
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: rs3135050; hg19: chr6-29628437;