rs3095293

Positions:

• chr6-29660564-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_206809.4(MOG):​c.436+898A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0055 (6 hom., cov: 0)
• Consequence: MOG NM_206809.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.145

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 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00553 (300/54264) while in subpopulation EAS AF= 0.0285 (54/1894). AF 95% confidence interval is 0.0224. There are 6 homozygotes in gnomad4. There are 134 alleles in male gnomad4 subpopulation. Median coverage is 0. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 300 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MOG	NM_206809.4	c.436+898A>G		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+898A>G		intron_variant		1	NM_206809.4	ENSP00000366115.3

Frequencies

GnomAD3 genomes AF: 0.00553 AC: 300 AN: 54242 Hom.: 6 Cov.: 0

Gnomad AFR AF: 0.00190

Gnomad AMI AF: 0.00543

Gnomad AMR AF: 0.00796

Gnomad ASJ AF: 0.0307

Gnomad EAS AF: 0.0285

Gnomad SAS AF: 0.0284

Gnomad FIN AF: 0.000741

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00532

Gnomad OTH AF: 0.0118

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

GnomAD4 genome AF: 0.00553 AC: 300 AN: 54264 Hom.: 6 Cov.: 0 AF XY: 0.00510 AC XY: 134 AN XY: 26252

Gnomad4 AFR AF: 0.00190

Gnomad4 AMR AF: 0.00796

Gnomad4 ASJ AF: 0.0307

Gnomad4 EAS AF: 0.0285

Gnomad4 SAS AF: 0.0284

Gnomad4 FIN AF: 0.000741

Gnomad4 NFE AF: 0.00532

Gnomad4 OTH AF: 0.0118

Alfa AF: 0.00674 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.2
DANN	Benign	0.56

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: rs3095293; hg19: chr6-29628341;