Genetic Variant MOG:n.*1180C>T (chr6-29671999-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 ENST00000376889.3(MOG):n.*1180C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0809 in 156,402 control chromosomes in the GnomAD database, including 672 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 0.081 ( 645 hom., cov: 32)

Exomes 𝑓: 0.086 ( 27 hom. )

Consequence

MOG
ENST00000376889.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.854

Publications

25 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=-0.96).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000376889.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
MOG	NM_206809.4	MANE Select	c.*814C>T	3_prime_UTR	Exon 8 of 8	NP_996532.2
MOG	NM_001363610.2		c.*1120C>T	3_prime_UTR	Exon 7 of 7	NP_001350539.1
MOG	NM_002433.5		c.*549C>T	3_prime_UTR	Exon 8 of 8	NP_002424.3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
MOG	ENST00000376889.3	TSL:1	n.*1180C>T	non_coding_transcript_exon	Exon 8 of 8	ENSP00000366086.3
MOG	ENST00000376917.8	TSL:1 MANE Select	c.*814C>T	3_prime_UTR	Exon 8 of 8	ENSP00000366115.3
MOG	ENST00000376894.8	TSL:1	c.*1120C>T	3_prime_UTR	Exon 7 of 7	ENSP00000366091.4

Frequencies

GnomAD3 genomes

AF:

0.0809

AC:

12289

AN:

151940

Hom.:

645

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0231

Gnomad AMI

AF:

0.118

Gnomad AMR

AF:

0.0920

Gnomad ASJ

AF:

0.169

Gnomad EAS

AF:

0.0187

Gnomad SAS

AF:

0.0312

Gnomad FIN

AF:

0.0865

Gnomad MID

AF:

0.0949

Gnomad NFE

AF:

0.115

Gnomad OTH

AF:

0.0933

GnomAD4 exome

AF:

0.0861

AC:

374

AN:

4344

Hom.:

Cov.:

AF XY:

0.0751

AC XY:

177

AN XY:

2356

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AF:

0.0787

AC:

AN:

1004

Ashkenazi Jewish (ASJ)

AF:

0.192

AC:

AN:

East Asian (EAS)

AF:

0.00641

AC:

AN:

156

South Asian (SAS)

AF:

0.0263

AC:

AN:

342

European-Finnish (FIN)

AF:

0.100

AC:

AN:

Middle Eastern (MID)

AF:

0.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.102

AC:

269

AN:

2630

Other (OTH)

AF:

0.0692

AC:

AN:

130

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.0808

AC:

12282

AN:

152058

Hom.:

645

Cov.:

AF XY:

0.0796

AC XY:

5917

AN XY:

74336

show subpopulations

African (AFR)

AF:

0.0230

AC:

956

AN:

41500

American (AMR)

AF:

0.0918

AC:

1401

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.169

AC:

588

AN:

3470

East Asian (EAS)

AF:

0.0187

AC:

AN:

5176

South Asian (SAS)

AF:

0.0308

AC:

148

AN:

4808

European-Finnish (FIN)

AF:

0.0865

AC:

915

AN:

10578

Middle Eastern (MID)

AF:

0.0986

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.115

AC:

7847

AN:

67954

Other (OTH)

AF:

0.0919

AC:

194

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.495

Heterozygous variant carriers

569

1138

1708

2277

2846

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

136

272

408

544

680

<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:

0.106

Hom.:

3191

Bravo

AF:

0.0782

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

0.17

(source)

DANN

Benign

0.89

PhyloP100

-0.85

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over