6-29672244-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_206809.4(MOG):c.*1059T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.876 in 161,116 control chromosomes in the GnomAD database, including 62,379 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.88 (58874 hom., cov: 27)
  • Exomes 𝑓: 0.85 (3505 hom.)
• Consequence: MOG NM_206809.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -3.52

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BP6: Variant 6-29672244-T-C is Benign according to our data. Variant chr6-29672244-T-C is described in ClinVar as [Benign]. Clinvar id is 1290020.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MOG	NM_206809.4	c.*1059T>C		3_prime_UTR_variant	8/8	ENST00000376917.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MOG	ENST00000376917.8	c.*1059T>C		3_prime_UTR_variant	8/8	1	NM_206809.4	P1
MOG	ENST00000376894.8	c.*1365T>C		3_prime_UTR_variant	7/7	1
MOG	ENST00000376889.3	c.*1425T>C		3_prime_UTR_variant, NMD_transcript_variant	8/8	1
MOG	ENST00000431798.6	c.*1059T>C		3_prime_UTR_variant	7/7	5

Frequencies

GnomAD3 genomes AF: 0.878 AC: 132880 AN: 151306 Hom.: 58809 Cov.: 27

Gnomad AFR AF: 0.956

Gnomad AMI AF: 0.847

Gnomad AMR AF: 0.915

Gnomad ASJ AF: 0.898

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.935

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.838

Gnomad OTH AF: 0.892

GnomAD4 exome AF: 0.847 AC: 8212 AN: 9696 Hom.: 3505 Cov.: 2 AF XY: 0.844 AC XY: 4933 AN XY: 5844

Gnomad4 AFR exome AF: 0.944

Gnomad4 AMR exome AF: 0.940

Gnomad4 ASJ exome AF: 0.862

Gnomad4 EAS exome AF: 0.995

Gnomad4 SAS exome AF: 0.884

Gnomad4 FIN exome AF: 0.665

Gnomad4 NFE exome AF: 0.831

Gnomad4 OTH exome AF: 0.851

GnomAD4 genome AF: 0.878 AC: 133003 AN: 151420 Hom.: 58874 Cov.: 27 AF XY: 0.874 AC XY: 64628 AN XY: 73920

Gnomad4 AFR AF: 0.956

Gnomad4 AMR AF: 0.915

Gnomad4 ASJ AF: 0.898

Gnomad4 EAS AF: 0.986

Gnomad4 SAS AF: 0.936

Gnomad4 FIN AF: 0.691

Gnomad4 NFE AF: 0.838

Gnomad4 OTH AF: 0.893

Alfa AF: 0.858 Hom.: 6973

Bravo AF: 0.899

Asia WGS AF: 0.956 AC: 3324 AN: 3476

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

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.43
Dann	Benign	0.27

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3135049; hg19: chr6-29640021;