6-29661567-T-C

Position:

• chr6-29661567-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.436+1901T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.217 in 983,712 control chromosomes in the GnomAD database, including 24,212 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 0.17 (2522 hom., cov: 31)
  • Exomes 𝑓: 0.23 (21690 hom.)
• Consequence: MOG NM_206809.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.580

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.312 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MOG	NM_206809.4	c.436+1901T>C		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+1901T>C		intron_variant		1	NM_206809.4	ENSP00000366115.3

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25227 AN: 151862 Hom.: 2510 Cov.: 31

Gnomad AFR AF: 0.0677

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.180

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.325

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.159

GnomAD4 exome AF: 0.226 AC: 187981 AN: 831732 Hom.: 21690 Cov.: 23 AF XY: 0.226 AC XY: 86913 AN XY: 384118

Gnomad4 AFR exome AF: 0.0558

Gnomad4 AMR exome AF: 0.259

Gnomad4 ASJ exome AF: 0.165

Gnomad4 EAS exome AF: 0.323

Gnomad4 SAS exome AF: 0.313

Gnomad4 FIN exome AF: 0.127

Gnomad4 NFE exome AF: 0.227

Gnomad4 OTH exome AF: 0.245

GnomAD4 genome AF: 0.166 AC: 25254 AN: 151980 Hom.: 2522 Cov.: 31 AF XY: 0.166 AC XY: 12311 AN XY: 74278

Gnomad4 AFR AF: 0.0677

Gnomad4 AMR AF: 0.181

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.325

Gnomad4 SAS AF: 0.311

Gnomad4 FIN AF: 0.126

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.168

Alfa AF: 0.0850 Hom.: 127

Bravo AF: 0.161

Asia WGS AF: 0.384 AC: 1338 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	4.7
DANN	Benign	0.65

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: rs3130251; hg19: chr6-29629344;