Genetic Variant ENST00000376894.8:c.795A>G (chr6-29670786-A-G) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS2

The ENST00000376894.8(MOG):c.795A>G(p.Thr265Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00135 in 1,601,004 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.0022 ( 8 hom., cov: 32)

Exomes 𝑓: 0.0013 ( 5 hom. )

Consequence

MOG
ENST00000376894.8 synonymous

Scores

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: -0.547

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 -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BP6

Variant 6-29670786-A-G is Benign according to our data. Variant chr6-29670786-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 3033947.Status of the report is no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=-0.547 with no splicing effect.

BS2

High AC in GnomAd4 at 337 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MOG	NM_206809.4 link	c.730+65A>G		intron_variant	Intron 7 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.730+65A>G		intron_variant	Intron 7 of 7	1	NM_206809.4	ENSP00000366115.3		Q16653-1

Frequencies

GnomAD3 genomes

AF:

0.00217

AC:

330

AN:

152222

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00203

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00641

Gnomad ASJ

AF:

0.000289

Gnomad EAS

AF:

0.000577

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.000377

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.00184

Gnomad OTH

AF:

0.00430

GnomAD3 exomes

AF:

0.00158

AC:

352

AN:

222384

Hom.:

AF XY:

0.00159

AC XY:

192

AN XY:

121016

show subpopulations

Gnomad AFR exome

AF:

0.00120

Gnomad AMR exome

AF:

0.00213

Gnomad ASJ exome

AF:

0.000107

Gnomad EAS exome

AF:

0.00273

Gnomad SAS exome

AF:

0.000355

Gnomad FIN exome

AF:

0.0000485

Gnomad NFE exome

AF:

0.00201

Gnomad OTH exome

AF:

0.00283

GnomAD4 exome

AF:

0.00125

AC:

1817

AN:

1448664

Hom.:

Cov.:

AF XY:

0.00126

AC XY:

910

AN XY:

719446

show subpopulations

Gnomad4 AFR exome

AF:

0.00206

Gnomad4 AMR exome

AF:

0.00226

Gnomad4 ASJ exome

AF:

0.000194

Gnomad4 EAS exome

AF:

0.00134

Gnomad4 SAS exome

AF:

0.000260

Gnomad4 FIN exome

AF:

0.0000966

Gnomad4 NFE exome

AF:

0.00126

Gnomad4 OTH exome

AF:

0.00172

GnomAD4 genome

AF:

0.00221

AC:

337

AN:

152340

Hom.:

Cov.:

AF XY:

0.00243

AC XY:

181

AN XY:

74502

show subpopulations

Gnomad4 AFR

AF:

0.00221

Gnomad4 AMR

AF:

0.00640

Gnomad4 ASJ

AF:

0.000289

Gnomad4 EAS

AF:

0.000579

Gnomad4 SAS

AF:

0.000207

Gnomad4 FIN

AF:

0.000377

Gnomad4 NFE

AF:

0.00184

Gnomad4 OTH

AF:

0.00426

Alfa

AF:

0.00175

Hom.:

Bravo

AF:

0.00232

Asia WGS

AF:

0.00318

AC:

AN:

3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

MOG-related disorder

Benign:1

May 15, 2020

PreventionGenetics, part of Exact Sciences

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

6.4

DANN

Benign

0.75

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over