rs2071652

Positions:

• chr6-29667540-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.551-103C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0463 in 1,181,212 control chromosomes in the GnomAD database, including 2,031 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 0.046 (207 hom., cov: 32)
  • Exomes 𝑓: 0.046 (1824 hom.)
• Consequence: MOG NM_206809.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.253

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MOG	NM_206809.4	c.551-103C>T		intron_variant		ENST00000376917.8	NP_996532.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MOG	ENST00000376917.8	c.551-103C>T		intron_variant		1	NM_206809.4	ENSP00000366115.3

Frequencies

GnomAD3 genomes AF: 0.0459 AC: 6979 AN: 152036 Hom.: 207 Cov.: 32

Gnomad AFR AF: 0.0560

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.0326

Gnomad ASJ AF: 0.0467

Gnomad EAS AF: 0.120

Gnomad SAS AF: 0.0953

Gnomad FIN AF: 0.0307

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0354

Gnomad OTH AF: 0.0484

GnomAD4 exome AF: 0.0464 AC: 47723 AN: 1029058 Hom.: 1824 AF XY: 0.0486 AC XY: 25830 AN XY: 531416

Gnomad4 AFR exome AF: 0.0529

Gnomad4 AMR exome AF: 0.0299

Gnomad4 ASJ exome AF: 0.0503

Gnomad4 EAS exome AF: 0.185

Gnomad4 SAS exome AF: 0.0968

Gnomad4 FIN exome AF: 0.0278

Gnomad4 NFE exome AF: 0.0354

Gnomad4 OTH exome AF: 0.0446

GnomAD4 genome AF: 0.0458 AC: 6976 AN: 152154 Hom.: 207 Cov.: 32 AF XY: 0.0459 AC XY: 3416 AN XY: 74378

Gnomad4 AFR AF: 0.0560

Gnomad4 AMR AF: 0.0325

Gnomad4 ASJ AF: 0.0467

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.0954

Gnomad4 FIN AF: 0.0307

Gnomad4 NFE AF: 0.0354

Gnomad4 OTH AF: 0.0479

Alfa AF: 0.0363 Hom.: 75

Bravo AF: 0.0457

Asia WGS AF: 0.0870 AC: 301 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.7
DANN	Benign	0.80

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: rs2071652; hg19: chr6-29635317; COSMIC: COSV65306732; COSMIC: COSV65306732;