rs2535261

Variant names:

• chr6-29660525-G-A
• rs2535261
• NM_206809.4:c.436+859G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-29660525-G-A
• chr6-29660525-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_206809.4(MOG):​c.436+859G>A 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 0.17 (2048 hom., cov: 20)
• Consequence: MOG NM_206809.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29
• 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=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.269 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MOG	NM_206809.4	c.436+859G>A		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+859G>A		intron_variant	Intron 2 of 7	1	NM_206809.4	ENSP00000366115.3

Frequencies

GnomAD3 genomes AF: 0.168 AC: 20635 AN: 123150 Hom.: 2046 Cov.: 20

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.235

Gnomad NFE AF: 0.127

Gnomad OTH AF: 0.173

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

GnomAD4 genome AF: 0.168 AC: 20652 AN: 123224 Hom.: 2048 Cov.: 20 AF XY: 0.171 AC XY: 9858 AN XY: 57514

African (AFR) AF: 0.274 AC: 8832 AN: 32224

American (AMR) AF: 0.115 AC: 1221 AN: 10634

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 354 AN: 3190

East Asian (EAS) AF: 0.205 AC: 861 AN: 4202

South Asian (SAS) AF: 0.168 AC: 551 AN: 3274

European-Finnish (FIN) AF: 0.113 AC: 669 AN: 5904

Middle Eastern (MID) AF: 0.234 AC: 52 AN: 222

European-Non Finnish (NFE) AF: 0.127 AC: 7764 AN: 61232

Other (OTH) AF: 0.170 AC: 261 AN: 1534

Alfa AF: 0.0192 Hom.: 21

Bravo AF: 0.172

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.65
DANN	Benign	0.35
PhyloP100		-2.3
Mutation Taster		=100/0	polymorphism (auto)

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: rs2535261; hg19: chr6-29628302;