rs2857783

chr6-29663811-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.437-2341T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.053 in 152,266 control chromosomes in the GnomAD database, including 433 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 0.053 (433 hom., cov: 32)
• Consequence: MOG NM_206809.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MOG	NM_206809.4	c.437-2341T>C		intron_variant		ENST00000376917.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MOG	ENST00000376917.8	c.437-2341T>C		intron_variant		1	NM_206809.4	P1

Frequencies

GnomAD3 genomes AF: 0.0530 AC: 8063 AN: 152148 Hom.: 431 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0411

Gnomad ASJ AF: 0.0285

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.00600

Gnomad FIN AF: 0.00254

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0207

Gnomad OTH AF: 0.0607

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

GnomAD4 genome AF: 0.0530 AC: 8072 AN: 152266 Hom.: 433 Cov.: 32 AF XY: 0.0506 AC XY: 3772 AN XY: 74472

Gnomad4 AFR AF: 0.138

Gnomad4 AMR AF: 0.0410

Gnomad4 ASJ AF: 0.0285

Gnomad4 EAS AF: 0.00270

Gnomad4 SAS AF: 0.00580

Gnomad4 FIN AF: 0.00254

Gnomad4 NFE AF: 0.0207

Gnomad4 OTH AF: 0.0596

Alfa AF: 0.0310 Hom.: 87

Bravo AF: 0.0609

Asia WGS AF: 0.0160 AC: 55 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.9
Dann	Benign	0.67

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: rs2857783; hg19: chr6-29631588;