chr6-29657224-A-C

Variant names:

• chr6-29657224-A-C
• rs3130250
• NM_206809.4:c.15A>C

Variant summary

Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_001363610.2(MOG):​c.15A>C​(p.Ser5Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000343 in 1,458,668 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 29)
  • Exomes 𝑓: 0.0000034 (0 hom.)
• Consequence: MOG NM_001363610.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.422
• Publications: 40 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: Likely_benign. The variant received -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BP7: Synonymous conserved (PhyloP=-0.422 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001363610.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MOG	NM_206809.4	MANE Select	c.15A>C	p.Ser5Ser	synonymous	Exon 1 of 8	NP_996532.2
	MOG	NM_001363610.2		c.15A>C	p.Ser5Ser	synonymous	Exon 1 of 7	NP_001350539.1
	MOG	NM_002433.5		c.15A>C	p.Ser5Ser	synonymous	Exon 1 of 8	NP_002424.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MOG	ENST00000376917.8	TSL:1 MANE Select	c.15A>C	p.Ser5Ser	synonymous	Exon 1 of 8	ENSP00000366115.3
	MOG	ENST00000376894.8	TSL:1	c.15A>C	p.Ser5Ser	synonymous	Exon 1 of 7	ENSP00000366091.4
	MOG	ENST00000376898.7	TSL:1	c.15A>C	p.Ser5Ser	synonymous	Exon 1 of 8	ENSP00000366095.3

Frequencies

GnomAD3 genomes Cov.: 29

GnomAD4 exome AF: 0.00000343 AC: 5 AN: 1458668 Hom.: 0 Cov.: 42 AF XY: 0.00000413 AC XY: 3 AN XY: 725604

African (AFR) AF: 0.00 AC: 0 AN: 33442

American (AMR) AF: 0.00 AC: 0 AN: 44592

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26072

East Asian (EAS) AF: 0.00 AC: 0 AN: 39696

South Asian (SAS) AF: 0.00 AC: 0 AN: 85986

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 52254

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5762

European-Non Finnish (NFE) AF: 0.00000450 AC: 5 AN: 1110548

Other (OTH) AF: 0.00 AC: 0 AN: 60316

GnomAD4 genome Cov.: 29

Alfa AF: 0.00 Hom.: 218694

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.96
DANN	Benign	0.47
PhyloP100		-0.42
PromoterAI		-0.0081	Neutral

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: rs3130250; hg19: chr6-29625001;