chr6-29672289-AAAAT-A

Position:

• chr6-29672289-AAAAT-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_206809.4(MOG):​c.*1148_*1151del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.21 in 167,622 control chromosomes in the GnomAD database, including 3,831 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.21 (3292 hom., cov: 0)
  • Exomes 𝑓: 0.19 (539 hom.)
• Consequence: MOG NM_206809.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.556

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 -10 ACMG points.

• BP6: Variant 6-29672289-AAAAT-A is Benign according to our data. Variant chr6-29672289-AAAAT-A is described in ClinVar as [Benign]. Clinvar id is 1249969.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MOG	NM_206809.4	c.*1148_*1151del		3_prime_UTR_variant	8/8	ENST00000376917.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MOG	ENST00000376917.8	c.*1148_*1151del		3_prime_UTR_variant	8/8	1	NM_206809.4	P1
MOG	ENST00000376894.8	c.*1454_*1457del		3_prime_UTR_variant	7/7	1
MOG	ENST00000376889.3	c.*1514_*1517del		3_prime_UTR_variant, NMD_transcript_variant	8/8	1
MOG	ENST00000431798.6	c.*1148_*1151del		3_prime_UTR_variant	7/7	5

Frequencies

GnomAD3 genomes AF: 0.214 AC: 29583 AN: 138042 Hom.: 3290 Cov.: 0

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.247

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.217

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.205

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.181

GnomAD4 exome AF: 0.190 AC: 5599 AN: 29538 Hom.: 539 AF XY: 0.191 AC XY: 3150 AN XY: 16500

Gnomad4 AFR exome AF: 0.155

Gnomad4 AMR exome AF: 0.175

Gnomad4 ASJ exome AF: 0.196

Gnomad4 EAS exome AF: 0.214

Gnomad4 SAS exome AF: 0.136

Gnomad4 FIN exome AF: 0.325

Gnomad4 NFE exome AF: 0.186

Gnomad4 OTH exome AF: 0.184

GnomAD4 genome AF: 0.214 AC: 29590 AN: 138084 Hom.: 3292 Cov.: 0 AF XY: 0.218 AC XY: 14435 AN XY: 66214

Gnomad4 AFR AF: 0.197

Gnomad4 AMR AF: 0.179

Gnomad4 ASJ AF: 0.217

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.177

Gnomad4 FIN AF: 0.313

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.181

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2021

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs200245124; hg19: chr6-29640066;