chr6-29658599-T-C

Variant names:

• chr6-29658599-T-C
• rs9257932
• NM_206809.4:c.89-720T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NM_206809.4(MOG):​c.89-720T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0305 in 152,240 control chromosomes in the GnomAD database, including 93 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 0.030 (93 hom., cov: 32)
• Consequence: MOG NM_206809.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.135

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BS1: Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0305 (4641/152240) while in subpopulation AFR AF= 0.0376 (1561/41544). AF 95% confidence interval is 0.036. There are 93 homozygotes in gnomad4. There are 2186 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High AC in GnomAd4 at 4641 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MOG	NM_206809.4	c.89-720T>C		intron_variant	Intron 1 of 7	ENST00000376917.8	NP_996532.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MOG	ENST00000376917.8	c.89-720T>C		intron_variant	Intron 1 of 7	1	NM_206809.4	ENSP00000366115.3

Frequencies

GnomAD3 genomes AF: 0.0305 AC: 4642 AN: 152122 Hom.: 93 Cov.: 32

Gnomad AFR AF: 0.0377

Gnomad AMI AF: 0.0604

Gnomad AMR AF: 0.0221

Gnomad ASJ AF: 0.0248

Gnomad EAS AF: 0.0369

Gnomad SAS AF: 0.0332

Gnomad FIN AF: 0.0298

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0275

Gnomad OTH AF: 0.0287

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

GnomAD4 genome AF: 0.0305 AC: 4641 AN: 152240 Hom.: 93 Cov.: 32 AF XY: 0.0294 AC XY: 2186 AN XY: 74420

Gnomad4 AFR AF: 0.0376

Gnomad4 AMR AF: 0.0221

Gnomad4 ASJ AF: 0.0248

Gnomad4 EAS AF: 0.0370

Gnomad4 SAS AF: 0.0330

Gnomad4 FIN AF: 0.0298

Gnomad4 NFE AF: 0.0275

Gnomad4 OTH AF: 0.0284

Alfa AF: 0.0274 Hom.: 10

Bravo AF: 0.0299

Asia WGS AF: 0.0200 AC: 69 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.6
DANN	Benign	0.74

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

Other links and lift over

dbSNP: rs9257932; hg19: chr6-29626376;