rs3095294

Positions:

• chr6-29660260-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.436+594G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 151,466 control chromosomes in the GnomAD database, including 3,134 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 (3134 hom., cov: 29)
• Consequence: MOG NM_206809.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.96

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=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MOG	NM_206809.4	c.436+594G>A		intron_variant		ENST00000376917.8	NP_996532.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MOG	ENST00000376917.8	c.436+594G>A		intron_variant		1	NM_206809.4	ENSP00000366115.3

Frequencies

GnomAD3 genomes AF: 0.192 AC: 29052 AN: 151348 Hom.: 3117 Cov.: 29

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.329

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.192 AC: 29091 AN: 151466 Hom.: 3134 Cov.: 29 AF XY: 0.191 AC XY: 14148 AN XY: 73952

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.319

Gnomad4 FIN AF: 0.149

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.187

Alfa AF: 0.196 Hom.: 365

Bravo AF: 0.191

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.7
DANN	Benign	0.74

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: rs3095294; hg19: chr6-29628037; COSMIC: COSV65320825; COSMIC: COSV65320825;