chr6-29664541-C-T

Position:

• chr6-29664541-C-T

Variant summary

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

The NM_206809.4(MOG):​c.437-1611C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 416,250 control chromosomes in the GnomAD database, including 9,966 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 0.20 (3204 hom., cov: 31)
  • Exomes 𝑓: 0.21 (6762 hom.)
• Consequence: MOG NM_206809.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MOG	NM_206809.4	c.437-1611C>T		intron_variant		ENST00000376917.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MOG	ENST00000376917.8	c.437-1611C>T		intron_variant		1	NM_206809.4	P1

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29693 AN: 151652 Hom.: 3203 Cov.: 31

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.265

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.273

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.293

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.161

GnomAD4 exome AF: 0.210 AC: 55516 AN: 264484 Hom.: 6762 AF XY: 0.198 AC XY: 30264 AN XY: 152558

Gnomad4 AFR exome AF: 0.106

Gnomad4 AMR exome AF: 0.265

Gnomad4 ASJ exome AF: 0.154

Gnomad4 EAS exome AF: 0.273

Gnomad4 SAS exome AF: 0.106

Gnomad4 FIN exome AF: 0.302

Gnomad4 NFE exome AF: 0.239

Gnomad4 OTH exome AF: 0.206

GnomAD4 genome AF: 0.196 AC: 29697 AN: 151766 Hom.: 3204 Cov.: 31 AF XY: 0.196 AC XY: 14545 AN XY: 74130

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.199

Gnomad4 ASJ AF: 0.157

Gnomad4 EAS AF: 0.272

Gnomad4 SAS AF: 0.111

Gnomad4 FIN AF: 0.293

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.160

Alfa AF: 0.217 Hom.: 5285

Bravo AF: 0.188

Asia WGS AF: 0.165 AC: 574 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.8
DANN	Benign	0.84

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: rs2256266; hg19: chr6-29632318;