Genetic Variant MOG:c.437-1611C>T (chr6-29664541-C-T) – 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.437-1611C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 416,250 control chromosomes in the GnomAD database, including 9,966 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 0.20 ( 3204 hom., cov: 31)

Exomes 𝑓: 0.21 ( 6762 hom. )

Consequence

MOG
NM_206809.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.212

Publications

26 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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.261 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MOG	NM_206809.4 link	c.437-1611C>T		intron_variant	Intron 2 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.437-1611C>T		intron_variant	Intron 2 of 7	1	NM_206809.4	ENSP00000366115.3		Q16653-1

Frequencies

GnomAD3 genomes

AF:

0.196

AC:

29693

AN:

151652

Hom.:

3203

Cov.:

show subpopulations

Gnomad AFR

AF:

0.115

Gnomad AMI

AF:

0.265

Gnomad AMR

AF:

0.199

Gnomad ASJ

AF:

0.157

Gnomad EAS

AF:

0.273

Gnomad SAS

AF:

0.111

Gnomad FIN

AF:

0.293

Gnomad MID

AF:

0.114

Gnomad NFE

AF:

0.232

Gnomad OTH

AF:

0.161

GnomAD4 exome

AF:

0.210

AC:

55516

AN:

264484

Hom.:

6762

AF XY:

0.198

AC XY:

30264

AN XY:

152558

show subpopulations

African (AFR)

AF:

0.106

AC:

586

AN:

5552

American (AMR)

AF:

0.265

AC:

5745

AN:

21696

Ashkenazi Jewish (ASJ)

AF:

0.154

AC:

1353

AN:

8766

East Asian (EAS)

AF:

0.273

AC:

1858

AN:

6800

South Asian (SAS)

AF:

0.106

AC:

5729

AN:

53902

European-Finnish (FIN)

AF:

0.302

AC:

3521

AN:

11678

Middle Eastern (MID)

AF:

0.103

AC:

100

AN:

968

European-Non Finnish (NFE)

AF:

0.239

AC:

34113

AN:

142950

Other (OTH)

AF:

0.206

AC:

2511

AN:

12172

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1911

3822

5733

7644

9555

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

184

368

552

736

920

<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:

0.196

AC:

29697

AN:

151766

Hom.:

3204

Cov.:

AF XY:

0.196

AC XY:

14545

AN XY:

74130

show subpopulations

African (AFR)

AF:

0.115

AC:

4753

AN:

41358

American (AMR)

AF:

0.199

AC:

3034

AN:

15232

Ashkenazi Jewish (ASJ)

AF:

0.157

AC:

546

AN:

3470

East Asian (EAS)

AF:

0.272

AC:

1407

AN:

5164

South Asian (SAS)

AF:

0.111

AC:

535

AN:

4806

European-Finnish (FIN)

AF:

0.293

AC:

3071

AN:

10488

Middle Eastern (MID)

AF:

0.116

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.232

AC:

15740

AN:

67940

Other (OTH)

AF:

0.160

AC:

337

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1203

2406

3610

4813

6016

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

308

616

924

1232

1540

<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:

0.215

Hom.:

13487

Bravo

AF:

0.188

Asia WGS

AF:

0.165

AC:

574

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

2.8

(source)

DANN

Benign

0.84

PhyloP100

0.21

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