dbSNP rs1318631: MOG:c.571+68G>A (chr6-29667731-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_206809.4(MOG):c.571+68G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.218 in 1,587,292 control chromosomes in the GnomAD database, including 39,764 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 0.19 ( 3162 hom., cov: 32)

Exomes 𝑓: 0.22 ( 36602 hom. )

Consequence

MOG
NM_206809.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.19

Variant links:

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MOG	NM_206809.4 link	c.571+68G>A		intron_variant	Intron 4 of 7	ENST00000376917.8	NP_996532.2	Q16653-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MOG	ENST00000376917.8 link	c.571+68G>A		intron_variant	Intron 4 of 7	1	NM_206809.4	ENSP00000366115.3		Q16653-1

Frequencies

GnomAD3 genomes

AF:

0.194

AC:

29541

AN:

152004

Hom.:

3161

Cov.:

show subpopulations

Gnomad AFR

AF:

0.115

Gnomad AMI

AF:

0.266

Gnomad AMR

AF:

0.184

Gnomad ASJ

AF:

0.158

Gnomad EAS

AF:

0.274

Gnomad SAS

AF:

0.111

Gnomad FIN

AF:

0.293

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.232

Gnomad OTH

AF:

0.159

GnomAD4 exome

AF:

0.220

AC:

316370

AN:

1435170

Hom.:

36602

Cov.:

AF XY:

0.217

AC XY:

155472

AN XY:

715724

show subpopulations

Gnomad4 AFR exome

AF:

0.107

Gnomad4 AMR exome

AF:

0.238

Gnomad4 ASJ exome

AF:

0.156

Gnomad4 EAS exome

AF:

0.267

Gnomad4 SAS exome

AF:

0.104

Gnomad4 FIN exome

AF:

0.301

Gnomad4 NFE exome

AF:

0.230

Gnomad4 OTH exome

AF:

0.202

GnomAD4 genome

AF:

0.194

AC:

29547

AN:

152122

Hom.:

3162

Cov.:

AF XY:

0.195

AC XY:

14493

AN XY:

74362

show subpopulations

Gnomad4 AFR

AF:

0.115

Gnomad4 AMR

AF:

0.184

Gnomad4 ASJ

AF:

0.158

Gnomad4 EAS

AF:

0.273

Gnomad4 SAS

AF:

0.111

Gnomad4 FIN

AF:

0.293

Gnomad4 NFE

AF:

0.232

Gnomad4 OTH

AF:

0.158

Alfa

AF:

0.217

Hom.:

4087

Bravo

AF:

0.186

Asia WGS

AF:

0.164

AC:

570

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

0.41

DANN

Benign

0.66

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over