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

Variant summary

Our verdict is Benign. The variant received -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

Publications

21 publications found

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 Gene-Disease associations (from GenCC):

narcolepsy 7
Inheritance: Unknown Classification: LIMITED Submitted by: Labcorp Genetics (formerly Invitae)

MOG links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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

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

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

African (AFR)

AF:

0.107

AC:

3529

AN:

32922

American (AMR)

AF:

0.238

AC:

10637

AN:

44688

Ashkenazi Jewish (ASJ)

AF:

0.156

AC:

4042

AN:

25970

East Asian (EAS)

AF:

0.267

AC:

10556

AN:

39586

South Asian (SAS)

AF:

0.104

AC:

8954

AN:

85718

European-Finnish (FIN)

AF:

0.301

AC:

16070

AN:

53314

Middle Eastern (MID)

AF:

0.126

AC:

723

AN:

5722

European-Non Finnish (NFE)

AF:

0.230

AC:

249836

AN:

1087756

Other (OTH)

AF:

0.202

AC:

12023

AN:

59494

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

13516

27032

40549

54065

67581

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8358

16716

25074

33432

41790

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.194

AC:

29547

AN:

152122

Hom.:

3162

Cov.:

AF XY:

0.195

AC XY:

14493

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.115

AC:

4786

AN:

41508

American (AMR)

AF:

0.184

AC:

2805

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.158

AC:

547

AN:

3470

East Asian (EAS)

AF:

0.273

AC:

1414

AN:

5172

South Asian (SAS)

AF:

0.111

AC:

537

AN:

4822

European-Finnish (FIN)

AF:

0.293

AC:

3098

AN:

10590

Middle Eastern (MID)

AF:

0.116

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.232

AC:

15749

AN:

67960

Other (OTH)

AF:

0.158

AC:

334

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1193

2386

3579

4772

5965

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

306

612

918

1224

1530

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.212

Hom.:

5277

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

(source)

DANN

Benign

0.66

PhyloP100

-1.2

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over