chr6-29660564-A-G

Variant names:

• chr6-29660564-A-G
• rs3095293
• NM_206809.4:c.436+898A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_206809.4(MOG):​c.436+898A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.0055 (6 hom., cov: 0)
• Consequence: MOG NM_206809.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.145
• Publications: 1 publications found

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)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BS1: Variant frequency is greater than expected in population eas. GnomAd4 allele frequency = 0.00553 (300/54264) while in subpopulation EAS AF = 0.0285 (54/1894). AF 95% confidence interval is 0.0224. There are 6 homozygotes in GnomAd4. There are 134 alleles in the male GnomAd4 subpopulation. Median coverage is 0. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 6 Unknown gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MOG	NM_206809.4	c.436+898A>G		intron_variant	Intron 2 of 7	ENST00000376917.8	NP_996532.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MOG	ENST00000376917.8	c.436+898A>G		intron_variant	Intron 2 of 7	1	NM_206809.4	ENSP00000366115.3

Frequencies

GnomAD3 genomes AF: 0.00553 AC: 300 AN: 54242 Hom.: 6 Cov.: 0

Gnomad AFR AF: 0.00190

Gnomad AMI AF: 0.00543

Gnomad AMR AF: 0.00796

Gnomad ASJ AF: 0.0307

Gnomad EAS AF: 0.0285

Gnomad SAS AF: 0.0284

Gnomad FIN AF: 0.000741

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00532

Gnomad OTH AF: 0.0118

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.00553 AC: 300 AN: 54264 Hom.: 6 Cov.: 0 AF XY: 0.00510 AC XY: 134 AN XY: 26252

African (AFR) AF: 0.00190 AC: 47 AN: 24802

American (AMR) AF: 0.00796 AC: 33 AN: 4144

Ashkenazi Jewish (ASJ) AF: 0.0307 AC: 28 AN: 912

East Asian (EAS) AF: 0.0285 AC: 54 AN: 1894

South Asian (SAS) AF: 0.0284 AC: 33 AN: 1164

European-Finnish (FIN) AF: 0.000741 AC: 2 AN: 2700

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 122

European-Non Finnish (NFE) AF: 0.00532 AC: 94 AN: 17662

Other (OTH) AF: 0.0118 AC: 8 AN: 680

Alfa AF: 0.00674 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.2
DANN	Benign	0.56
PhyloP100		-0.14

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

Other links and lift over

dbSNP: rs3095293; hg19: chr6-29628341;