rs1768208

Variant names:

• chr3-39481512-T-C
• rs1768208
• NM_001393704.1:c.-5+1389T>C

Your query was ambiguous. Multiple possible variants found:

• chr3-39481512-T-C
• chr3-39481512-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001393704.1(MOBP):​c.-5+1389T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.756 in 152,102 control chromosomes in the GnomAD database, including 44,844 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 0.76 (44844 hom., cov: 31)
• Consequence: MOBP NM_001393704.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03
• Publications: 61 publications found

Genes affected

MOBP (HGNC:7189): (myelin associated oligodendrocyte basic protein) Predicted to enable actin binding activity and myosin binding activity. Predicted to be a structural constituent of myelin sheath. Predicted to be involved in nervous system development. Predicted to be located in mitochondrion. Predicted to be active in cortical actin cytoskeleton. Implicated in frontotemporal dementia. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.933 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001393704.1. 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
	MOBP	NM_001393704.1	MANE Select	c.-5+1389T>C		intron	N/A	NP_001380633.1
	MOBP	NM_001278322.2		c.-5+1389T>C		intron	N/A	NP_001265251.1
	MOBP	NM_001278323.2		c.-5+13772T>C		intron	N/A	NP_001265252.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MOBP	ENST00000684792.1	MANE Select	c.-5+1389T>C		intron	N/A	ENSP00000508923.1
	MOBP	ENST00000383754.7	TSL:1	c.-5+1389T>C		intron	N/A	ENSP00000373261.3
	MOBP	ENST00000452959.6	TSL:1	n.-5+1389T>C		intron	N/A	ENSP00000405549.1

Frequencies

GnomAD3 genomes AF: 0.755 AC: 114809 AN: 151984 Hom.: 44785 Cov.: 31

Gnomad AFR AF: 0.940

Gnomad AMI AF: 0.618

Gnomad AMR AF: 0.625

Gnomad ASJ AF: 0.704

Gnomad EAS AF: 0.395

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.726

Gnomad OTH AF: 0.733

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

GnomAD4 genome AF: 0.756 AC: 114918 AN: 152102 Hom.: 44844 Cov.: 31 AF XY: 0.746 AC XY: 55466 AN XY: 74350

African (AFR) AF: 0.941 AC: 39046 AN: 41516

American (AMR) AF: 0.625 AC: 9543 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.704 AC: 2443 AN: 3470

East Asian (EAS) AF: 0.396 AC: 2049 AN: 5178

South Asian (SAS) AF: 0.665 AC: 3203 AN: 4816

European-Finnish (FIN) AF: 0.661 AC: 6970 AN: 10548

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.726 AC: 49380 AN: 67992

Other (OTH) AF: 0.729 AC: 1539 AN: 2110

Alfa AF: 0.725 Hom.: 131958

Bravo AF: 0.756

Asia WGS AF: 0.555 AC: 1933 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.69
PhyloP100		-1.0
Mutation Taster		=100/0	polymorphism (auto)

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: rs1768208; hg19: chr3-39523003;