chr6-29671999-C-T

Position:

• chr6-29671999-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_206809.4(MOG):​c.*814C>T variant causes a 3 prime UTR 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 NM_206809.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.854

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=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MOG	NM_206809.4	c.*814C>T		3_prime_UTR_variant	8/8	ENST00000376917.8	NP_996532.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MOG	ENST00000376917.8	c.*814C>T		3_prime_UTR_variant	8/8	1	NM_206809.4	ENSP00000366115	P1

Frequencies

GnomAD3 genomes AF: 0.0809 AC: 12289 AN: 151940 Hom.: 645 Cov.: 32

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.: 27 Cov.: 0 AF XY: 0.0751 AC XY: 177 AN XY: 2356

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0787

Gnomad4 ASJ exome AF: 0.192

Gnomad4 EAS exome AF: 0.00641

Gnomad4 SAS exome AF: 0.0263

Gnomad4 FIN exome AF: 0.100

Gnomad4 NFE exome AF: 0.102

Gnomad4 OTH exome AF: 0.0692

GnomAD4 genome AF: 0.0808 AC: 12282 AN: 152058 Hom.: 645 Cov.: 32 AF XY: 0.0796 AC XY: 5917 AN XY: 74336

Gnomad4 AFR AF: 0.0230

Gnomad4 AMR AF: 0.0918

Gnomad4 ASJ AF: 0.169

Gnomad4 EAS AF: 0.0187

Gnomad4 SAS AF: 0.0308

Gnomad4 FIN AF: 0.0865

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.0919

Alfa AF: 0.115 Hom.: 1255

Bravo AF: 0.0782

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.17
DANN	Benign	0.89

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9257936; hg19: chr6-29639776;