6-29657224-A-G

Position:

• chr6-29657224-A-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6 BP7 BA1

The NM_206809.4(MOG):​c.15A>G​(p.Ser5=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.856 in 1,609,366 control chromosomes in the GnomAD database, including 591,631 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in Lovd as Benign (no stars).

• Frequency:
  • Genomes: 𝑓 0.88 (58645 hom., cov: 29)
  • Exomes 𝑓: 0.85 (532986 hom.)
• Consequence: MOG NM_206809.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.422

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BP6: Variant 6-29657224-A-G is Benign according to our data. Variant chr6-29657224-A-G is described in Lovd as [Benign].
• BP7: Synonymous conserved (PhyloP=-0.422 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MOG	NM_206809.4	c.15A>G	p.Ser5=	synonymous_variant	1/8	ENST00000376917.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MOG	ENST00000376917.8	c.15A>G	p.Ser5=	synonymous_variant	1/8	1	NM_206809.4	P1

Frequencies

GnomAD3 genomes AF: 0.876 AC: 133039 AN: 151914 Hom.: 58597 Cov.: 29

Gnomad AFR AF: 0.934

Gnomad AMI AF: 0.856

Gnomad AMR AF: 0.915

Gnomad ASJ AF: 0.878

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.957

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.842

Gnomad OTH AF: 0.886

GnomAD3 exomes AF: 0.879 AC: 215352 AN: 245056 Hom.: 95186 AF XY: 0.878 AC XY: 117192 AN XY: 133434

Gnomad AFR exome AF: 0.937

Gnomad AMR exome AF: 0.941

Gnomad ASJ exome AF: 0.888

Gnomad EAS exome AF: 0.988

Gnomad SAS exome AF: 0.950

Gnomad FIN exome AF: 0.730

Gnomad NFE exome AF: 0.843

Gnomad OTH exome AF: 0.866

GnomAD4 exome AF: 0.854 AC: 1244192 AN: 1457334 Hom.: 532986 Cov.: 42 AF XY: 0.857 AC XY: 621206 AN XY: 725046

Gnomad4 AFR exome AF: 0.934

Gnomad4 AMR exome AF: 0.938

Gnomad4 ASJ exome AF: 0.887

Gnomad4 EAS exome AF: 0.992

Gnomad4 SAS exome AF: 0.947

Gnomad4 FIN exome AF: 0.739

Gnomad4 NFE exome AF: 0.839

Gnomad4 OTH exome AF: 0.868

GnomAD4 genome AF: 0.876 AC: 133146 AN: 152032 Hom.: 58645 Cov.: 29 AF XY: 0.873 AC XY: 64860 AN XY: 74300

Gnomad4 AFR AF: 0.934

Gnomad4 AMR AF: 0.915

Gnomad4 ASJ AF: 0.878

Gnomad4 EAS AF: 0.982

Gnomad4 SAS AF: 0.957

Gnomad4 FIN AF: 0.716

Gnomad4 NFE AF: 0.842

Gnomad4 OTH AF: 0.887

Alfa AF: 0.858 Hom.: 90822

Bravo AF: 0.893

Asia WGS AF: 0.962 AC: 3347 AN: 3478

EpiCase AF: 0.851

EpiControl AF: 0.856

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.98
DANN	Benign	0.48

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: rs3130250; hg19: chr6-29625001; COSMIC: COSV65320756; COSMIC: COSV65320756;