6-29660525-G-A

Position:

• chr6-29660525-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+859G>A 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 0.17 (2048 hom., cov: 20)
• Consequence: MOG NM_206809.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29

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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MOG	NM_206809.4	c.436+859G>A		intron_variant		ENST00000376917.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MOG	ENST00000376917.8	c.436+859G>A		intron_variant		1	NM_206809.4	P1

Frequencies

GnomAD3 genomes AF: 0.168 AC: 20635 AN: 123150 Hom.: 2046 Cov.: 20

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.235

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.168 AC: 20652 AN: 123224 Hom.: 2048 Cov.: 20 AF XY: 0.171 AC XY: 9858 AN XY: 57514

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.115

Gnomad4 ASJ AF: 0.111

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.168

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.127

Gnomad4 OTH AF: 0.170

Bravo AF: 0.172

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.65
DANN	Benign	0.35

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: rs2535261; hg19: chr6-29628302;