chr6-29659172-C-G

Position:

• chr6-29659172-C-G

Variant summary

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

The NM_206809.4(MOG):​c.89-147C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.149 in 719,312 control chromosomes in the GnomAD database, including 9,107 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 0.18 (3042 hom., cov: 31)
  • Exomes 𝑓: 0.14 (6065 hom.)
• Consequence: MOG NM_206809.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.23

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=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.297 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MOG	NM_206809.4	c.89-147C>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.89-147C>G		intron_variant		1	NM_206809.4	ENSP00000366115.3

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28051 AN: 151830 Hom.: 3039 Cov.: 31

Gnomad AFR AF: 0.301

Gnomad AMI AF: 0.106

Gnomad AMR AF: 0.146

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.191

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.188

GnomAD4 exome AF: 0.140 AC: 79348 AN: 567364 Hom.: 6065 AF XY: 0.142 AC XY: 43324 AN XY: 304134

Gnomad4 AFR exome AF: 0.307

Gnomad4 AMR exome AF: 0.114

Gnomad4 ASJ exome AF: 0.158

Gnomad4 EAS exome AF: 0.105

Gnomad4 SAS exome AF: 0.175

Gnomad4 FIN exome AF: 0.116

Gnomad4 NFE exome AF: 0.133

Gnomad4 OTH exome AF: 0.151

GnomAD4 genome AF: 0.185 AC: 28079 AN: 151948 Hom.: 3042 Cov.: 31 AF XY: 0.185 AC XY: 13729 AN XY: 74292

Gnomad4 AFR AF: 0.302

Gnomad4 AMR AF: 0.146

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.191

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.137

Gnomad4 OTH AF: 0.185

Alfa AF: 0.0691 Hom.: 81

Bravo AF: 0.195

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.053
DANN	Benign	0.31

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: rs16895223; hg19: chr6-29626949;